Sequence
atgc intronic sequence ATGC exonic sequence...tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
---tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgta--cagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
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gatttttaataagaattaatgctt---gtatttgcgtct-caacatggaggcttcatgtgctcttgttc-tgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 5
tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagt-taatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
| | | | | | || || |||| | | ||| | || |||| | | |||| | | ||| || | ||| | | |||||||| ||||| ||||||||||| || |||||||| || |||||||| |||||||||||||||||||||||||| || |||||||||||||| |||||||
taagaattaattcttgtat-ttgcatctcaacatggaggcctcctgtattctatgctcttgttctgaagaggaaataacctcctcatcattttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
tcatatgca-gtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatt-tatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
| | || || | ||| | || | | || | | | ||||| | | || | | | | | || | || |||||||||| || ||||| || || ||||| ||||| | ||| ||||| || ||||||||| |||| || ||||| || ||||||||||| | || || |
--agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
-tcatatgcagtgttagtgcattcaatctttctgc-ttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
| || ||||| | || | || || | | || | | | | | | || | || ||| || | | ||||||| || || ||||| ||||| ||||| ||||| | ||| ||||| || ||||||||| |||| |||||||| || ||||||||||| | || || |
tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttctt--aaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctc-ctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
| | | | | | | || | ||| | ||| | | | | ||| | || | | | | |||||||| |||||||||||||| || ||||||||||| | || ||||| || |||||||| |||||||| ||||| || ||||||||||| | || || |
-ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------tcatatgcagtgttagtgcattcaatctttctgct-tatggctcttaagttatatggaagttaatgaatataggaaaacttctcc-tgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
|| | |||||||| || | ||||| | | ||| | || || |||| | | | || | | |||| ||| || | | ||||||| || || ||||| || || ||||||||||||| || ||||||||||||||||| |||||| | ||||| || |||||||| || || |||||||
gttagtgctatgattattatgctcgt-tgcagtgtagccctcttgattctttatacagtatcctttgtatattttatg----cttgtaatcttatgcccatttctatgtgttatg-gtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
agttaat putative branch site (score: 4)
cttctcctgtcattt putative PPT
aagttaatgaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-catatgc
- - - - - - - - tgcattc
- - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaa