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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacttgggggcttgatttgggtactgggcagtcgaatgccgcacctctttgtttggttttcgagtacttcatttgacatgtttttttctatttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGATTTGGTTTTTCACCTGGAGCTTATTCGATTTTCCGAGCTGAAGTTGTGGA

Basic information

species Physcomitrella patens
transcript PP1S323_56V6.1
intron # 1
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|18342284|gb|BJ174319.1|BJ174319
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18354659|gb|BJ186717.1|BJ186717
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18329029|gb|BJ161035.1|BJ161035
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18343035|gb|BJ175072.1|BJ175072
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18348792|gb|BJ180841.1|BJ180841
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18342315|gb|BJ174350.1|BJ174350
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18355759|gb|BJ187818.1|BJ187818
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18348448|gb|BJ180497.1|BJ180497
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18358579|gb|BJ190638.1|BJ190638
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|208361492|gb|DC942791.1|DC942791
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|208353585|gb|DC938736.1|DC938736
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATTGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18342603|gb|BJ174638.1|BJ174638
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|208358235|gb|DC934512.1|DC934512
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
EST: gi|18352817|gb|BJ184872.1|BJ184872
EST:     GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAG                         GCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT
genomic: GGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGAT

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: 35 (upstream exon), 32 (downstream exon)
Score: 7

CTTGGACTCCAGCCATAGCCGATTCAGTTCCTTGTGGACGTGCACGAGGTGGCTGCCGTTCCTCATTAAGGGCATGATCGTCCTCTCGTCTTGTCTACAGgtagttgttt ... atttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGATTTGGTTTTTCACCTGGAGCTTATTCGATTTTCCGAGCTGAAGTTGTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttgtttggttttcgagtacttcatttgacatgtttttttctatttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGATTTGGTTTTTCACCTGGAGCTTATTCGATTTTCCGAGCTGAAGTTGTGGA
                          atttgac  putative branch site (score: 7)
                                  tgtttttttctatttc  CT-rich tract
                                 atgtttttttctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacttgggggcttgatttgggtactgggcagtcgaatgccgcacctctttgtttggttttcgagtacttcatttgacatgtttttttctatttcgacagGCACCTTAGTGGCTTTTACCATCACTTCCACGAAGCTTTTTATTCAACGATTTGGTTTTTCACCTGGAGCTTATTCGATTTTCCGAGCTGAAGTTGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - -tgccgca