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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttattcctctgtcaatctttttcttaatatgcagtttgatataaggaaatgtctggtcaattcctttacttaaggaatcatgcaaggtttaccct...

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 4
GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttattcctctgtcaatctttttcttaatatgcagtttgatataaggaaatgtctggtcaattcctttacttaaggaatcatgcaaggtttaccct----------
||||| || || || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  ||||||||  ||| ||   | |  |  | ||| ||| || |   |||   | |       | |||  ||| | | |      |  | |||   ||    |||   |          
GTGGGTGCGGATAACAATCTACTTGTAAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGAGgtatgtt-ttatgccgcaatacctttgcttcattttttgttcatttt-------tttcttctcattccatgagagcagtgcatcgctcataacttagttttcctgtgcag

upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA10G30220.1 (Glycine max), 5'ss of exon 4
GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttattcctctgtca-atctttttcttaatatgcagtttgatataaggaaatgtctggtcaattcctttacttaaggaatcatgcaaggtttaccct
||||| ||||| || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  |||| |||  ||| ||   |||  | | |||  |     | ||    || || |  |   ||   |  | | ||  ||| ||   | |                   
GTGGGTGCAGAAAACAATCTACTTGTGAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGTGgtatgtt-ttatgctgctataccttgcttcatttttgttcatttatttttgtgcattgttcataacttagttttctggtgcag------------------
















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|100389821|gb|BY971173.1|BY971173
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAA
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAA
EST: gi|162165520|gb|FC340631.1|FC340631
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100447940|gb|CJ972239.1|CJ972239
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162155413|gb|FC332027.1|FC332027
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|18327722|gb|BJ159725.1|BJ159725
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100396902|gb|BY953885.1|BY953885
EST:     CTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTTGGAG                         AGGTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCG
genomic: CTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTT-GGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCG
EST: gi|208399548|gb|DC908545.1|DC908545
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162151154|gb|FC327153.1|FC327153
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162198693|gb|FC373474.1|FC373474
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100423760|gb|BY976531.1|BY976531
EST:     CTCAAGGATCACACTCACACTTTTTATTAACAAAAGCGGCAACGTTGGAG                         AGTTGGACCTTCAGATTTCCCGTGTGGAGAACCTCTTGCACGGGTATAAAA
genomic: CTCAAGGATCACACTCACACTTTT-ATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGAC-TTCAGATTTCCAGTG-GGAGCACCTCT-GCACGGC-ATAAAA
EST: gi|208351706|gb|DC910066.1|DC910066
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGTGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100367017|gb|BY948326.1|BY948326
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162167140|gb|FC343616.1|FC343616
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162159709|gb|FC336095.1|FC336095
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162167477|gb|FC344194.1|FC344194
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|208349541|gb|DC905651.1|DC905651
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100390582|gb|BY971337.1|BY971337
EST:     TCAAGGATCACACTCACACTTTTTATTAACAAAGGCGGCAAACGTTGGAG                         AGCTGGACTTCAGATTTCCAGGGGGAGCAC
genomic: TCAAGGATCACACTCACACTTTT-ATTAACAAAGGCGGCAA-CGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCAC
EST: gi|100387464|gb|BY988335.1|BY988335
EST:     ACTCAGGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCT
EST: gi|208397089|gb|DC908103.1|DC908103
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAA-GCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162168664|gb|FC343926.1|FC343926
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162170376|gb|FC346781.1|FC346781
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162176795|gb|FC352809.1|FC352809
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|162267926|gb|FC444007.1|FC444007
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100450706|gb|CJ974398.1|CJ974398
EST:     CTCAAGGATCACACTCACACTTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTNCAAATT-CCAGTGGGAGCACCTCTGCACGNCATAAAAGCGT
genomic: CTCAAGGATCACACTCACACTTTT-ATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
EST: gi|100443101|gb|BY981727.1|BY981727
EST:     CTNCA-GGATCACACTCACACTTTTATTAACAAAGGCNGCAACGGTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGC
genomic: CT-CAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGC
EST: gi|162166539|gb|FC343236.1|FC343236
EST:     ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG                         AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT
genomic: ACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGT

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: 29 (upstream exon), 33 (downstream exon)
Score: 17

GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttatt ... tcttccgcagAGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAGgttagttattcctctgtcaatctttttcttaatatgcagtttgatataaggaaatgtctggtcaattcctttacttaaggaatcatgcaaggtttaccct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG