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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctttttagagtcatttaataggagttttttcgtttcgtctggacctaatttacgagttccttttatatttggccccagctccactatggatcgatagtgcggaccatgaaatggttcattaacccgctgcatttcctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGGTGTGAGGCTGTTCCTTGTGAACAGTTTGAAGCTGCTTTTCAG

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
intron # 2
splice site 3'
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:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100415542|gb|BY992893.1|BY992893
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|162196647|gb|FC374937.1|FC374937
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|208360694|gb|DC930491.1|DC930491
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|67577989|gb|BJ950156.1|BJ950156
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTA
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTA
EST: gi|208363461|gb|DC939708.1|DC939708
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100429013|gb|BY977896.1|BY977896
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTCCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100416557|gb|BY975446.1|BY975446
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|208376666|gb|DC932130.1|DC932130
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100407545|gb|BY991747.1|BY991747
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|208356936|gb|DC942682.1|DC942682
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100372584|gb|BY948605.1|BY948605
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100379968|gb|BY968780.1|BY968780
EST:     TTTGGCCTTACCACCCCAG-CATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: TTTGGCCTTACCACCC-AGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100394488|gb|BY972090.1|BY972090
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100371232|gb|BY986003.1|BY986003
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100405446|gb|BY955529.1|BY955529
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|208362206|gb|DC939630.1|DC939630
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100382155|gb|BY969020.1|BY969020
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
EST: gi|100451701|gb|CJ974898.1|CJ974898
EST:     ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAG                         GGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG
genomic: ATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGG

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: 32 (upstream exon), 33 (downstream exon)
Score: 3

AGCCTTTGTCCATCACCGATTTGGCCTTACCACCCAGGCATGGATCTGATTTACGTGTAGCTTATCAGgtatcttttt ... cctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGGTGTGAGGCTGTTCCTTGTGAACAGTTTGAAGCTGCTTTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgatagtgcggaccatgaaatggttcattaacccgctgcatttcctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGGTGTGAGGCTGTTCCTTGTGAACAGTTTGAAGCTGCTTTTCAG
                           cattaac  putative branch site (score: 3)
                                     ctgcatttccttttt  putative PPT
                                               tttttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctttttagagtcatttaataggagttttttcgtttcgtctggacctaatttacgagttccttttatatttggccccagctccactatggatcgatagtgcggaccatgaaatggttcattaacccgctgcatttcctttttaagGGTGTTCCTGGAGCTTACAGTGAAGCAGCTGCTGCTAAAGCATATCCTAGGTGTGAGGCTGTTCCTTGTGAACAGTTTGAAGCTGCTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT