Sequence
atgc intronic sequence ATGC exonic sequencegtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
Basic information
species | Physcomitrella patens |
transcript | PP1S425_2V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 7
gtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgt-tttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
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--------------------------------------aaaactcaa-atgtgaaat-atgtgtaacttttgtggatggagggagt--atcatctatctgcccaatgtatttatcgatattatttta--ttgtattgtgt---gcagAGGTGATAACATCTGCTGAGTTCCACCCTACTCACTGTAATACATTGGCTTATAGTAGCTCAAAGGGCTCCATTCGACTTGTTGACCTGAGGCAGTCAGC
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 7
gtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaa--cagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
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----------------------------------------------gctttcctttattgtttttatcacatattctttgagt--ttctactggtggcatctttgttgttagctactgatagctatggttttgttctatcacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACCCACTGCAATACGTTGGCATATAGTAGCTCTAAGGGATCCATTCGACTTGTTGATCTGCGCCAATCAGC
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
gtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
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-----gctttcctttattgtttttatca--catatccgttaagtt------tctactggt-----ggcatctctgttgttagctgctgat-----agttattctttggttctatgacat-----------------------gcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
gattgat putative branch site (score: 4)
atgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG