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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCCTCTACTCAGATTGAGGAAGGGAACCCCGAGCAAATCTGGGGCACTAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaaatcaaagattgtatttcagcagaatttaacgaaacgatagtggaatgagtagtatggtgcatgtgtaccgaaaagtcatcggtcaccatt...

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162182473|gb|FC357448.1|FC357448
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100415542|gb|BY992893.1|BY992893
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|162196647|gb|FC374937.1|FC374937
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|208360694|gb|DC930491.1|DC930491
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|67577989|gb|BJ950156.1|BJ950156
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|208363461|gb|DC939708.1|DC939708
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100429013|gb|BY977896.1|BY977896
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100416557|gb|BY975446.1|BY975446
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|208376666|gb|DC932130.1|DC932130
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100407545|gb|BY991747.1|BY991747
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|208356936|gb|DC942682.1|DC942682
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100372584|gb|BY948605.1|BY948605
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100379968|gb|BY968780.1|BY968780
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCCAG-CATGGATCTGAT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCC-AGGCATGGATCTGAT
EST: gi|100394488|gb|BY972090.1|BY972090
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100371232|gb|BY986003.1|BY986003
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100405446|gb|BY955529.1|BY955529
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|208362206|gb|DC939630.1|DC939630
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100382155|gb|BY969020.1|BY969020
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
EST: gi|100451701|gb|CJ974898.1|CJ974898
EST:     TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTA                         AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT
genomic: TAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 27 (upstream exon), 35 (downstream exon)
Score: 10

GCCTCCTCTACTCAGATTGAGGAAGGGAACCCCGAGCAAATCTGGGGCACTAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaa ... ggttgaccagAGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCCTCTACTCAGATTGAGGAAGGGAACCCCGAGCAAATCTGGGGCACTAACGCGCCGGTGGTTTCTACGACCGAGCTAGTCAGCCTAACACTACCTAgtaagtgcaaatcaaagattgtatttcagcagaatttaacgaaacgatagtggaatgagtagtatggtgcatgtgtaccgaaaagtcatcggtcaccatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaaa