Sequence
atgc intronic sequence ATGC exonic sequence...aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
Basic information
species | Physcomitrella patens |
transcript | PP1S12_19V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S12_19V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 5
----------------------aaaattttgatcacgattttgatttgatattgggtgatgaatata-attagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGAC-CTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
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gtatcttattttctcctttatctgtagtcagttcaatttccttgtcaaatgctcatcagcttatgtggagtaaaggaattatgatgcccatgtgcgtaccctaaaacatttcgttaat--cagGTAGTAAACATGGAGTGGGGGAATTTCTGGTCATCACATTTGCCAAGGACGCCATATG-ACATCTTGCTGGATGATGAAACACACAATCGCAATGATCAG
upper sequence: PP1S12_19V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G068913_T01 (Zea mays), 3'ss of exon 5
--aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgttgtaatatagcatctaatttgtagcatatgact--attga-cagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
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gtattattctc-ttgctgctttgctctgtatccaaattatcaatatcatcgat--ttatcctgtggacaaagatgtagttcttattcaatcgttcaattcatcagGTTGTAAACATGGAATGGGGCAATTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACGCAAAATCGCAATGATCAG
upper sequence: PP1S12_19V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 5
-----aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
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gtaagtaggttatgaatatgtgtgagacttaatttcttgtgt--gatagagttat---ccttattgtgatacaaagcatg-ctgattacttctaaatatt-atagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
upper sequence: PP1S12_19V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA05G35890.1 (Glycine max), 3'ss of exon 5
-----aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgt-tgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
| || ||| || | ||||| | | ||| ||| | || |||| ||| ||| | | | | | | | | |||| | |||||||||||||||||||||| |||||| | ||||| || | |||| || | ||| | |||| ||||| || || || |||||| |
gtaagtaggttatgaatgcgtgtgagatttagtttcttgtgt--gatagatttgtccttattgtgtgtgatacaaagcatg-ctgattacttctaagtatt-atagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTGAGAGCTTAAACCCTGGAGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
atctaat putative branch site (score: 3)
tttgttgtaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA