Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttgagctttctgaatgatcagagtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggacaagtatcacataattttcccacaaccttgttagtatgaattcatgcttacactgtcattggttgtgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG
Basic information
species | Physcomitrella patens |
transcript | PP1S139_9V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S139_9V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 3'ss of exon 7
gtaagtttttgagctttctgaatgatcagagtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggacaagtatcacataattttcccacaaccttgttagtatgaattcatgcttacactgtcattggttgtgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG--
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-----------------------------------------------------------------gtatg---tatctttgagtttatactataccacttccctatgtttatgttttgctcagccaatgcttactct--tgctacatttgatttttagGGCTATGGTTCCTTTCTGTTGCGAGATCTACCATTTGATGCTATTCAGTTTTGCATATATGAGCAACTTCGAATAGGCTAT--AAACTGGCG
upper sequence: PP1S139_9V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 7
--gtaagtttttgagctttctgaatgatcag-agtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggac-aagtatcacataattttcccacaaccttgttagtatgaattcatgcttacactgtcattggttg----tgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG--
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gtatgtgtattctggcatcttatttggttaacaatctttatattgactt--ctgtttgaaggatgaattactgatttactgttgatctgaggtgtaaattttgttcctattttaaatatatcttgtgataatatccattatatcaccggtttcttttggtttgtagGGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTA--CAAACTTGTG
upper sequence: PP1S139_9V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0157g00180.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtttttgagctttctgaatgatcagagtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggaca-agtat-cacataattttcccacaaccttgttagtatgaat-tcatgcttacactgtcattggttgtgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG
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-------------------------------------------------------------tttcgatgagattattcatgaatgcagtatatttctgtagttcatgtattattattggtgcattcatcttgattattttttattttttgggagattgcagGGATATGGATCCTTTTTATTGCGAGATTTACCTTTTGATGCTCTCCAGTTTTGCATCTATGAGCAGCTACGGATAGGGTATAAGCTAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaaccttgttagtatgaattcatgcttacactgtcattggttgtgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG
tgcttac putative branch site (score: 2)
tatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttgagctttctgaatgatcagagtctccatgcttatatgattcttttgcgtgtgttcgtccgccctgcccgtggacaagtatcacataattttcccacaaccttgttagtatgaattcatgcttacactgtcattggttgtgatttacagGGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA