Sequence
atgc intronic sequence ATGC exonic sequence...catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g33070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052606_T01 (Zea mays), 3'ss of exon 1
catagctatagctaagcttggataataattcttgacagaaacatc-----tcgtttgctcactga-tgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
|| || || || | | ||||||||| ||| ||| | | | || | || ||||| ||| | | ||| |||| ||||||||||||||| ||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| | ||| |
---gtacgtacgtacgcatgacactttctctctgacagaaagatcctggatcgatcgtttgcttactgtgaaatcaaccctcacttgcgacatta---tattccagGTGGTCTCAGATTGCTGCCCGGTTGCCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGGCTCAAGAACAGCTCGGCA
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
catagcta-tagctaagcttgg-ataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
|| || || || | || | || | | | |||| || | | | || | | | || | | | || ||| ||||||||||| || || || || || || ||||| ||||| ||||||||||| |||||||||||||| | ||||| | | || || | |
--taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G05080.1 (Glycine max), 3'ss of exon 1
catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaatta--ttgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
| | || | ||| | ||| || | || | || | | || || | || | | | | | | | ||||| | ||| |||||||| || || || || || || || ||||| ||||| ||||||||||| |||||||||||||| | ||||| | | || || | |
-gttgttagcattttcattgtaatata-ttttggatgttattgccttttgttttctcttcttttaagttttaaccatttccaagttgtaaattaaatctcagATGGTCTCAAATTGCCGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACACTGAAGAAAAGGTTGAAAATGAACAACAAT
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G36630.1 (Glycine max), 3'ss of exon 1
--catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
| | || || || | | | | || | | | | | |||||| || ||| | | | | || ||||||||||||||| || || || || || || ||||| ||||| ||||| ||||| |||||||||||||| | ||||| | | || | | | |||
attagaactctatgtaggatatg-tggtatatgagtatattgg-gtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTCCACATTGAAGAAAAGGTTGAAAACTAACACTTCC
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0064g00960.t01 (Vitis vinifera), 3'ss of exon 1
--catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
| || ||| | | | | || | | | ||| || | |||| | | ||| | | | | | ||| || |||||||||||||||||| || || ||||| ||| | |||||||| || || ||||||||||||||||| ||||||||||| | || || | | ||
agtaggtcttaagcataattaatgtgaaaaatgaaaaaaaaaatgcagatttatttggttgattacacttctcattttccatt-tgtttcaaatggtt-cagGTGGTCTCAGATCGCGGCGCGCCTACCAGGGAGGACCGACAATGAAATAAAGAACTTCTGGAACTCTACCATCAAGAAAAGGCTGAAAAACAGCTTGCAG
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
---catagctatagctaagcttggataataattcttgaca-gaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
| || | | || | | | ||| | |||| || ||| | || | | ||| | | || | | || ||||||||||| ||||| || | | || || || ||||| ||||||||||||||||||||||||||||| |||||||||| ||| | | |
gatgagagattctgtcaacccttgtgaatgg---tcgacatgatacaacattgttatttttaattttttaatttttaaaatta-gtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 2
catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccg-tactacgacgcatggaattat-tgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGC-GCCTCAAGATCTCCTCCTCC
| || | | |||| | || | | | | | | | | | | | || | | | | | | | || || ||||||||||||||||| || | | | |||| || |||||||||||||| ||||| ||||||||||||||| ||||||||| || || | || | ||
ctgagacac-gataaggtcacatgttggtaataagct-atcccccccccccccccccccctgctagttgggctaatgcagcaattgatccccttgcatgcagGTGGTCTCAGATTGCAACTCAGTTACCAGGCCGCACCGACAACGAAATCAAAAACTTCTGGAACTCCTGTATCAAGAAGAAGCTTCGCAACATCGGCATC-
upper sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
-----catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctac-cgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCT-CAAGATCTCCTCCTCC
|| | | |||| || | || ||| |||| | | || | ||| | | | | | | || | || | || ||||||||||| ||||| || ||| |||||| || ||||| |||||||| || || |||||||||||||| |||||||||| || | | || | ||
tcatcgatgagaggcagaagggccggattgtagtctctg-cagctacatgtgctc--cttgcaaatgttgagttaaagcagaatttgat-cctgta--taatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
atgaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catagctatagctaagcttggataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - -gcttgga
- - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - agaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgga