Sequence
atgc intronic sequence ATGC exonic sequencegtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
Basic information
species | Physcomitrella patens |
transcript | PP1S44_339V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
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---------------------------------acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttgacct-gtatatgcatcatgacctttc-------ctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
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gtgaggttattgacctactgtatgtatttacgaatggtagattacat-gttcttg--ttttatatcgtaattgtaataactgttacctgtggctctctg-atatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G01190.1 (Glycine max), 3'ss of exon 12
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaataga---gtgaagtgaggctaatcctacaatgcgattgt-agATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
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---------------------------------------------------------gtttgtcactcatccttaaaaatattagtctatataatgattaatttatactcattacctcacatggaagatgcaaccaaatcttcagGTTGGGGGGGCTAGTGAGGCCGAAGTTGGGGAAAGGAAAGATAGAGTAACAGATGCTTTAAATGCCACTAGAGCAGCTGTGGAAGAGGGAATTGTTCCGG
upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G20560.2 (Glycine max), 3'ss of exon 11
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaataga-gtgaagtgaggctaatcctacaatgcgat-tgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
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---------------------------------------------------------gtttgtcactcatccttgagaatactagtatataatgattaatttatagtcatcatctcacatggaagatgcaaccaaatattcagGTTGGGGGGGCTAGTGAGGCCGAAGTTGGGGAAAGGAAAGATAGAGTAACAGATGCTTTAAATGCCACTAGAGCTGCTGTGGAAGAGGGAATTGTTCCAG
upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
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----------------------------gttagtccatg--ttataatgttttggga----gtcttagaatcatagcagcctggttgt----aagtgtcttgttataacttc-tggagctaattgtg---------tttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
ggctaat putative branch site (score: 3)
aaaatgtacaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG