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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacccttcccctcagaacgtctaatgtttcgtaactgaatgcatggagcggtttctaacaggctagaaatttcaggttctctattatcactgtgacatattgtagatgtcatcgcataccagttgtttaacattatttcaatcgtctttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_157V6.4 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 5
gttcacccttcccctcagaacgtctaatgtttcgtaactgaatgcatggagcggtttctaacaggctagaaatttcaggttctctattat-cactgtgacatattgtaga--tgtcatcgcataccagttgtttaacattatttcaatcgtctttattgc-agCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC
                                                              | | ||         ||||   | |  | |||   || | ||     |  |  ||  | |||  |||||| |       |||  || || | |  ||| |||| ||||||||||| ||||||||||| || ||||| || ||||| || ||||||||  | ||||| || ||||| |  ||  | ||  | ||  | || |
--------------------------------------------------------------aagttaatgtaactgggtttggtttggtgcacccagataaatgagcaatttaccagtgaatat-agttgtctcggtaactttgtattgtttgttctgctagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAAACGCTTATTGCAGGTGGTCCTTTCGTGCTTCCCCTTGCACACAAAC

upper sequence: PP1S62_157V6.4 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 5
gttcacccttcccctcagaacgtctaatgtttcgtaactgaatgcatggagcggtttctaacaggctagaaatttcaggttctctattatcactgtgac-atattgtagatgtcatcgcataccagttgtttaacattatttcaatcgtctttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC
                                                            | |  ||  || |||  | || |  |   | | |  ||  ||||   | | |  |     |  ||| || | ||  || || |  |  | |||| ||||||| || |||||||| |||||||| ||||||||||||||| | || || ||||| || ||||| || || ||||| |  ||  | ||  | ||||| || |
----------------------------------------------------------gtatatactctaattttttg-ttattaaaccttattaagaggatatgaaaaaagaaa----gttgcagatgataaagcttgttgc--ttatttttactgcagCCTACGGTTGCTGCAATTGAAGCAGGAAAGGACATTGCTCTTGCAAACAAAGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAAC
















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|162156416|gb|FC332648.1|FC332648
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|162168654|gb|FC343916.1|FC343916
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|162179792|gb|FC356383.1|FC356383
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|162250938|gb|FC425760.1|FC425760
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|208352746|gb|DC905880.1|DC905880
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|100442899|gb|BY963394.1|BY963394
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|162272851|gb|FC448007.1|FC448007
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|162208298|gb|FC384402.1|FC384402
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA
EST: gi|100379666|gb|BY949883.1|BY949883
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAAATAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAA-TAA
EST: gi|162163958|gb|FC339868.1|FC339868
EST:     CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGAAAGGATATTGCTTTGGCTAATAAA
genomic: CAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 58

GTGGCGAGGCATCCAGAAGCCGTCACTGTCGTCACAGGGATCGTTGGTTGCGCAGGATTGAAGgttcaccctt ... tttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagatgtcatcgcataccagttgtttaacattatttcaatcgtctttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC
                       gtttaac  putative branch site (score: 58)
                                        tcgtcttt  putative PPT
                        tttaacattatttcaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacccttcccctcagaacgtctaatgtttcgtaactgaatgcatggagcggtttctaacaggctagaaatttcaggttctctattatcactgtgacatattgtagatgtcatcgcataccagttgtttaacattatttcaatcgtctttattgcagCCCACAGTTGCTGCTATTGAAGCTGGAAAGGACATTGCTTTGGCTAATAAAGAAACCTTAATTGCTGGAGGTCCATATGTTTTGCCTTTGGCCAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC