Sequence
atgc intronic sequence ATGC exonic sequencegtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAGATAA
Basic information
species | Physcomitrella patens |
transcript | PP1S365_37V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S365_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G097995_T02 (Zea mays), 3'ss of exon 4
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAGATAA----------------------------------------
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--------------------------------gtaagatcatat--gctttactacttgtcttctttgtcttaaagctttcttaagctgaa----cttgtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA
upper sequence: PP1S365_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G22620.5 (Glycine max), 3'ss of exon 4
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGA--AAGAAGATAA--------------------------------------
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gtaagcatctacttctaa----------ttctaaacaactgtcatgcattttttattttatttttataaaaaatgatgatctgatgatattcttataccaatactcagGAAATGGTAGATTTTCTTGTGGATATATGGGAGCAAGATGGCCTATACGACTGAGATATTGAAGATTGAGGAAGTGCTGAAAATAATTCTAGTTCTTGCT
upper sequence: PP1S365_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G25360.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAG-ATAA---------------------------------------
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----------------------gtaagcatttttttctcagca--agtttacacattctataaacatga---ttaaggatttgatgatttaataataaactgtggcagGAAATGGTGGATTTTTTGGTGGATGTGTGGGAGCAAGAAGGCTTGTATGATTGATTTGCAACTCTTTAAACTTAATTTAGTTTCATCTTTTCTTTTATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAGATAA
cttcgtctt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAGATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG