[Experimental Setting] Experimenter: Christoph Bock Date of experiment: 29.04.2005 Project name: BiQ_Analyzer Beta Test Experiment No. / ID: 2 [Sample information] Organism: yeti horribilis Strain or subtype: himalaya Sex: male Tissue: heart [Sequence Location] - IMPORTANT - Please specify the exact genomic location of the analyzed sequence. Yeti Genome Draft - Acession No. YETI_123456, bp 100032-100151 Accession number of sequence: YETI_123456 Genome browser link: N/A Additional position information (if applicable): [Functional Elements] Please specify the sequence characteristics by ticking the appropriate box(es). ( ) intergenic ( ) repetitive element, please specify type (L1, ALU, etc.): ( ) upstream (2 - 10 kb upstream of transcriptional start site) ( ) promoter (2 kb upstream to 500 bp downstream of transcription start site) (X) exonic ( ) intronic Does the sequence relate to a gene? Please give its GO name: Gene Name: Invisible [Imprinting] Are there any allele-specific sequence polymorphisms present in sequence? Please tick. ( ) yes ( ) no If yes, please give its position and specify the polymorphism in detail: [Experimental details] Which primers where used? Please give their sequences: How was the experiment carried out? Please specify the protocol used and any deviations from it (or give a lab notebook cross-reference): [Quality control] Please roughly estimate the quality of your sequences: ( ) very good ( ) good ( ) average ( ) just acceptable ( ) poor What kind of quality problems are present in the sequences? Please specify type and degree: [Free comment (motivation / findings / problems / ...)] Please use this space to give any additional details relating to the experiment, its motivation, or its results: thanks to Reinhold Messner for providing the sample... ;-) [BiQ_Analyzer Documentation (automatically generated)] Date of quality check: 29 April 2005 Conversion type: C -> T Genomic Sequence (original): CCCGGGATCGCTCTCCCAGCAGGTGAAGCCTCGCCATGGACCCTCCCCGTCGGGGCCCCGCGCTGCCCCGCCCGCCCCCAGCCGCTGGCCAAGGCCGCGGTCGCGCAGGCGCAGTGCCGCGTCCCGCCGCCGCCCCGCCCTGCCCGTCGCTGCGGAAGGCGCCGCGCGCAGCAACGCGCACTTCCTCTCCAGGAATCCGCGGAGGGAGCGCAGGCTCGAAGAGCTCCTGGACG Genomic Sequence (fully converted): TTCGGGATCGTTTTTTTAGTAGGTGAAGTTTCGTTATGGATTTTTTTCGTCGGGGTTTCGCGTTGTTTCGTTCGTTTTTAGTCGTTGGTTAAGGTCGCGGTCGCGTAGGCGTAGTGTCGCGTTTCGTCGTCGTTTCGTTTTGTTCGTCGTTGCGGAAGGCGTCGCGCGTAGTAACGCGTATTTTTTTTTTAGGAATTCGCGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG [BiQ_Analyzer Quality Data (automatically generated)] List of the sequence identities relative to the genomic sequence (gaps ignored): Sequence [2]: 91% Sequence [3]: 99% Sequence [4]: 100% Sequence [5]: 100% Sequence [6]: 100% Sequence [7]: 100% Sequence [8]: 100% List of the sequences' conversion rates: Sequence [2]: 100% (67 out of 67) Sequence [3]: 96% (66 out of 69) Sequence [4]: 99% (68 out of 69) Sequence [5]: 90% (62 out of 69) Sequence [6]: 96% (66 out of 69) Sequence [7]: 100% (69 out of 69) Sequence [8]: 100% (69 out of 69)
CLUSTAL W (1.83) multiple sequence alignment Genomic_Sequence TTCGGGATCGTTTTTTT-AGTAGGTGAAGTTTCGTTATGGATTTTTTTCGTCGGGGTTTC [2]seq_A.seq TTCGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTC [3]seq_B.seq TTTGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT [4]seq_C.seq TTCGGGATCGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTCGTTGGGGTTTC [5]seq_D.seq TCCGGGATCGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTCTTTGTTGGGGTTTT [6]seq_E.seq TTTGGGATTGTTTTTTTTAGCAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT [7]seq_H.seq TTCGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTC [8]seq_I.seq TTTGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT * ***** ******** ** *********** ************ ** ** ******* Genomic_Sequence G-CGTTGTTTCGTTCGTTTTTAGTCGTTGGTT-AAGGTCGCGGTCGCGTAGGCGTAGTGT [2]seq_A.seq G-TGTTGTTTTGTTCGTTTTTTGTTGTTGGTT-AAGGAAAAAA------AAAAATAGTGT [3]seq_B.seq G-TGTTGTTTTGTTTGTTTTTAGTTGTTGGTT-AAGGTTGTGGTTGTGTAGCTGTAGTGT [4]seq_C.seq G-TGTTGTTTTGTTCGTTTTTAGTCGTTGGTT-AAGGTTGCGGTCGCGTAGGCGTAGTGT [5]seq_D.seq G-TGTTGTTTTGTTTGTCCTTAGTCGTTGGTT-AAGGTTGTGGTTGTGTAGGTGTGGTGT [6]seq_E.seq GATGTTGTTTCGTTTGTTTCTAGTTGTTGGTTTAAGGTCGTGGTTGTGTAGGCGTAGTGT [7]seq_H.seq G-TGTTGTTTTGTTCGTTTTTTGTTGTTGGTT-AAGGTCGCGGTCGCGTAGGCGTAGTGT [8]seq_I.seq G-TGTTGTTTTGTTTGTTTTTAGTTGTTGGTT-AAGGTTGTGGTTGTGTAGGTGTAGTGT * ******* *** ** * ** ******* **** * * **** Genomic_Sequence CGCGTTTCGTCGTCGTTTCGTTTTGTTCGTCGTTGCGGAAGGCG-TCGCGCGTAGTAACG [2]seq_A.seq CGCGTTTCGTCGTCGTTTAGTTTTGTTCGTGGTTGCGGAAGGCGGTTGCGCGTAGTAACG [3]seq_B.seq TGTGTTTTGTCGTTGTTTTGTTTTGTTTGTTGTTGTGGATGGTG-TTGTGTGTAGCAGTG [4]seq_C.seq CGCGTTCCGTCGTCGTTTCGTTTTGTTCGTTGTTGTGGAAGGTG-TTGCGCGTAGTAATG [5]seq_D.seq CGTGTCTTGTCGTCGTTCTGTTTTGTTTGTTGTTGCGGAAGGTG-TTGCGTGTAGCAACG [6]seq_E.seq CGCGTTTCGTCGTTGTTTTGTTTTGTTCGTCGTTGCGGAAGGTG-TTGTGCGTAGCAATG [7]seq_H.seq CGCGTTTCGTCGTCGTTTTGTTTTGTTCGTCGTTGCGGAAGGCGGTTGCGCGTAGTAACG [8]seq_I.seq TGTGTTTTGTTGTTGTTTTGTTTTGTTTGTTGTTGTGGAAGGTG-TTGTGTGTAGTAATG * ** ** ** *** ******** ** **** *** ** * * * * **** * * Genomic_Sequence CGTATTTTTTTTTT-AGGAATTCGCGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG [2]seq_A.seq TGTATTTTTTTTTT-AGGAATTAGTGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG [3]seq_B.seq TGTATTTTTTTTTC-AGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGCTTTTGGATG [4]seq_C.seq CGTATTTTTTTTTT-AGGAATTCGTGGAGGGAGTGTAGGTTCGAAGAGTTTTTGGATG [5]seq_D.seq TGTATTTTTTTTTT-AGGAATTCGCGGAGGGAGTGTAGGTTCGAAGAGTTTTTGGACG [6]seq_E.seq CGTATTTTTTTTTT-AGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGTTTTTGGATG [7]seq_H.seq TGTATTTTTTTTTT-AGGAATTTGTGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG [8]seq_I.seq TGTATTTTTTTTTTTAGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGTTTTTGGATG ************ ******* * ******** ******* ****** ******* *
Genomic Sequence with numbered CpG dinucleotides: 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 CCCGGGATCGCTCTCCC-AGCAGGTGAAGCCTCGCCATGGACCCTCCCCGTCGGGGCCCCG-CGCTGCCCCGCCCGCCCCCAGCCGCTGGCC-AAGGCCGCGGTCGCGCAGGCGCAGTGCCGCGTCCCGCCGCCGCCCCGCCCTGCCCGTCGCTGCGGAAGGCG-CCGCGCGCAGCAACGCGCACTTCCTCTCC-AGGAATCCGCGGAGGGAGCGCAGGCTCGAAGAGCTCCTGGACG Methylation data for these CpG dinucleotides (1=methylated, 0=unmethylated, x=unknown): Sequence_Identifier CpG_1 CpG_2 CpG_3 CpG_4 CpG_5 CpG_6 CpG_7 CpG_8 CpG_9 CpG_10 CpG_11 CpG_12 CpG_13 CpG_14 CpG_15 CpG_16 CpG_17 CpG_18 CpG_19 CpG_20 CpG_21 CpG_22 CpG_23 CpG_24 CpG_25 CpG_26 CpG_27 CpG_28 CpG_29 CpG_30 CpG_31 CpG_32 CpG_33 CpG_34 CpG_35 [2]seq_A.seq 1 0 0 0 0 1 0 0 1 0 x x x x x 1 1 1 1 1 x 1 x 1 1 0 1 1 1 0 x 0 1 1 1 [3]seq_B.seq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [4]seq_C.seq 1 1 0 1 0 1 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 0 1 1 0 0 1 0 [5]seq_D.seq 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 0 1 0 1 0 1 1 0 1 1 [6]seq_E.seq 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 1 1 0 0 1 1 1 0 0 0 1 0 1 0 0 0 0 0 [7]seq_H.seq 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 0 0 0 1 1 1 [8]seq_I.seq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0Explanation: each '1' corresponds to a methylated C, a '0' corresponds to a an unmethylated C, and an 'x' corresponds to a non-CpG position.
[2]seq_A.seq | --I-----O-----------------------O---------------O--O-------I--O-------O---I---------O-----------------------------------I-I----I--I--I-------------I-------I------I---O-I-I-------I-O-----------------------O--------I-------I--------------I- |
[3]seq_B.seq | --O-----O-----------------------O---------------O--O-------O--O-------O---O---------O-------------O-O---O-O-----O-------O-O----O--I--O----O--------O--O----O------O---O-O-O-------O-O---------------------O-O--------O-------O--------------O- |
[4]seq_C.seq | --I-----I-----------------------O---------------I--O-------I--O-------O---I---------I-------------O-I---I-I-----I-------I-I----I--I--I----I--------I--O----O------O---O-I-I-------O-I---------------------I-O--------O-------I--------------O- |
[5]seq_D.seq | --I-----I-----------------------O---------------O--O-------O--O-------O---O---------I-------------O-O---O-O-----O-------I-O----O--I--I----O--------O--O----I------O---O-I-O-------I-O---------------------I-I--------O-------I--------------I- |
[6]seq_E.seq | --O-----O-----------------------O---------------O--O-------O--O-------I---O---------O-------------I-O---O-O-----I-------I-I----I--I--O----O--------I--I----I------O---O-O-I-------O-I---------------------O-O--------O-------O--------------O- |
[7]seq_H.seq | --I-----O-----------------------O---------------O--O-------I--O-------O---I---------O-------------I-I---I-I-----I-------I-I----I--I--I----O--------I--I----I------I---O-I-I-------I-O---------------------O-O--------I-------I--------------I- |
[8]seq_I.seq | --O-----O-----------------------O---------------O--O-------O--O-------O---O---------O-------------O-O---O-O-----O-------O-O----O--O--O----O--------O--O----O------O---O-O-O-------O-O---------------------O-O--------O-------O--------------O- |
>Generated with BiQ_Analyzer by Christoph Bock