Sequence
atgc intronic sequence ATGC exonic sequence...tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171466_T01 (Zea mays), 3'ss of exon 1
----------tgtttggatttcgttaacggtgttaccttcagttcttgtagcaatt--actaata---gctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------
|| || || | | | | | ||||| | | ||| | | | || ||| | | |||||||| || | | || || | || ||| || || | | || | ||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
gtaacgacgacgtgtgtgttatctgttcccttctgcgttcagcacgcagacagatttaatttgcacgtgccagac--gtggactgatttg-agctgcggtg-tctcgctctgggcgtgta---gGCGCCGGCGCAACCGAGGGCACCAAGCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAG
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G40550.1 (Glycine max), 3'ss of exon 2
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctg--atttgcag----ttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------------
|| || || ||| || ||| ||| ||| ||| | | | || || || || | | || || | | | || | | | ||| || | | || || ||||||||||| || |||||||||||||| || || ||| ||||||| ||| ||||||| || || ||
---------------------tttgccctctgttgctgcagccatttctatgctctatttgtttggcttgttatctgttgaccttgttcataaattcgttttatttgactttgagattcagGTGGTGCTGAGGGTTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCAC
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G10480.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------tgtttggatttcgttaacg-gtgttaccttcagttcttgtagcaattactaatagctagatttatag----cctgat-ttgcagtt-ttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------
|| ||| || | | || | || | || ||| || ||| | |||| | |||| ||| || ||| || ||| | | |||| || || | || ||| | | |||||||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaa---gGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G10480.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------tgtttggatttcgttaacg-gtgttaccttcagttcttgtagcaattactaatagctagatttatag----cctgat-ttgcagtt-ttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG------------
|| ||| || | | || | || | || ||| || ||| | |||| | |||| ||| || ||| || ||| | | |||| || || | || ||| | | |||||||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaa---ggagCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGT
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------------
|| || ||| | || | ||| || | || ||||| | ||| | ||| || | | || | | | |||| |||||| || |||| | ||||| ||||||||||| || |||||||||||||||||||| ||| |||||||||| ||||||||||| || ||
---ctgtatccaattatc-----taattcttgtttacata-ctctttttaatattcaa--ttacaatgaagattgtccttgaatttatctcagttgggaaatgag----gtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
--tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG------
| | | || | ||| | | | | | | || | | | | || || | || | | ||| ||| || || |||| | |||| | || || |||||||||| | ||||||||||||||||||||||||||| |||||| || ||||| |||||||| ||
gctcagcgtctggcgctgtcggctgggcgagcgatgccagctttagtttcgtcggcccacagggat-gctgaacatggcgcatgtgtgatgttgg-ctgcagATGAGGAGGGTGGCGCTG------GCCGCGGCAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC
upper sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG--------------
|| | ||| | || || ||| ||| | || | | | |||| | ||||| ||| ||||||||||||||||||| ||||| ||| ||||||||| ||||| ||||| || ||
----------------------------------------------------------------------gttcctactttctttatgttt--cttccaggcgagGATGGAACGG--GGAAAT-------CGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG
tagatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - -ccttcag
- - - - - - - - - - - - - - - - - - tgtagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatga