Sequence
atgc intronic sequence ATGC exonic sequencegtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g24430.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 4
gtaattgcttaagattaaaatatatttggactaatccttcta-tggttgacacatacccttgtttataagcagttgacacatttttctt----caaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
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----atacatatacacaaaaaaga---gaagcaatcttaggaattatttacaggc-tattagttcataaacttttgtaaccttttccttttctctaatgcaatcttagGAATTCGAATTCGAAGAAGCTGATAAGGTGGCAGAATGCTACCCTCAAGGTTACCATGGGGTTGATAAGGAAGGCAGGCCTGTCTACTTTGAACGGCTTG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
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------------gtcctaaacat-tttaagatcatcttctttttctt------ctcctttaattaaagtc---tgatcctttttacttc--ttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacataccct-tgtttataa-gcagttgacacatttttcttcaaatcctatc--tcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
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-tacgtgcttc-gacaccagtacat----actgatttatgtgaggg-ggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21359 (Selaginella moellendorffii), 3'ss of exon 2
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
||| | | | ||| | || |||| | || | | || || | | ||||||| || |||| || || | ||| | ||| ||||||||||||| ||||||||||||| || ||||| ||||| | ||||| || || | |
------------------------------gtaaatgatatctcattg-tatatctttttgtc-----actgtgaggaaaacttcgtttgtgtac------agGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23906 (Selaginella moellendorffii), 3'ss of exon 2
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
||| | | | ||| | || ||||| | || | | || || | | ||||||| || |||| || || | ||| | ||| ||||||||||||| ||||||||||||| || ||||| ||||| | ||||| || || | |
------------------------------gtaaatgatatctcattg-tatatctttttgtt-----actgtgaggaaaacttcgtttgtgtac------agGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
agttgac putative branch site (score: 4)
tcctatctc putative PPT
atttttcttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacatacccttgtttataagcagttgacacatttttcttcaaatcctatctcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA