Sequence
atgc intronic sequence ATGC exonic sequencegttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S22_329V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaat-gagattgtaccaacttc-ttgactgctttctg-gacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
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------------------------------------------------------------------------------------------aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgt----------tcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
upper sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
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------------------------------------------------------------------------------------------gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgc----tcaactacaaatggactg--actcatctttctttttgaccct-cagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
upper sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G432083_T01 (Zea mays), 3'ss of exon 3
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacattt--cgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaa--tgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
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------------------------------------------------------------------------------------------------tcttgattcaatg---ctgggacaaagtactttttgttgttctagtgttcaaccaaaacaaactaacgccaaca--aactgacttgcatgttgaatgacctatagGGTGGTGGGCCATATTATCTTATAGGCCGTGCACTTGGTCCTGAAGTTGGAGTTAGTATAGGATTATGCTTCTTCCTCGGGAATGCAGTGGCTGGATCCA
upper sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgt-tgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
||| | | || | | | | || | | | | | | | | |||| || ||| | ||| || |||||||||| || |||||||| ||||| || || ||||||||||| ||||| || || || || || || || ||||||||||| |||||||| |||||
------------------------------------------------------------------------------------------------tttgtaaaaagaaaagcagttttttccccccaaaaaaat-ctaattctaacactcattaataattg-atatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
upper sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
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------------------------------------------------------------------------------------------aaagcagttta--ttaaaaaaaa-gaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattt---tcttgtgt-atgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
ggttaac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT