Sequence
atgc intronic sequence ATGC exonic sequencegtacaatgtgttcatgtgttggtataattttttaggaataactgaacctgaaattgctgtgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g13970.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G019358_T02 (Zea mays), 3'ss of exon 11
gtacaatgtgttcatgtgtt-----------ggtataattttttaggaataactgaacct-------gaaattgctgtgataattct-gtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
||| || | ||| | | || ||| || ||| | |||| | ||| || ||| ||||| ||| | |||||||||||||||||| ||||| || || |||| || |||||||||||||| |||||| | |||||||| || ||||| ||||||||||||||||| || |
gtatcatttcttcctttctttccccttcatcagta-aacgtttgaagaattggtaaactctcatctaaaagttgatgtgacgatttttgtagCTCATGTTTAGCAAATTTGAATACGATGGAATACTCAACCCAACATTTACTGAAGGTCCGTTTGAGCTTCCTTTTTCGAGTATTAGAGCATACATCAATG
upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 11
-----------------gtacaatgtgttcatgtgttggtataattttttaggaataactgaacctgaaattgctgtgataa----ttctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
| | ||| | | | | | ||| | | | | | || || || |||| |||||||||| ||||||||||||||||| || || | || ||| ||| |||||| |||||||||| || | || || || ||||| ||||
gtatcattacaggcatgactctgtatgtcttttggcttattagaaatttcacacttgttcttatttcttaatgatgaagcaaaactctctgcagCTCATGTTCAGCAAGTTTGAGTATGATGGTAAATTAAATGAAACTTTTGTGGAAGGTCCATTTGAGCTTCCAGTGTCTAGCATACATGCATATATAATAA
upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT4G18810.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacaatgtgttcatgtgttggtat-aattttttaggaataac-----tgaacctgaaattgctg---tgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
| |||| | || || | || | | ||| | | || | ||| | || ||| | |||| ||||||||||| ||||||||||| || ||||| ||||| ||||| | |||||| | || ||||| || || || || ||| |||| || || | |
-----gtttgttttcctttttgtgttaaccctcttaaaattcccattctaaatgtttgattaataagttggctatttttcagCTTATGTTTAGCAAATTTGAGTATGATGGTAAGCTTAACCCTACATTCAAAGAAGGACCTTTCGAGCTTCCTTTATCTAGCATTCGAGCTTATATCCAAG
upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 11
------------gtacaatgtgttcatgtgttggtataattttttaggaataactgaacctgaaattgctgtgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
| | ||| || | | | ||||||| || | || || | | | | |||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||| | ||||| ||||| |||| || | ||||| || || ||||| ||||| |
gcatgcttccatgcttattgttctcgttcagctttgtgattttttgctaagtttttgtt----gatgaatgcaaaattgttccagCTCATGTTCAGCAAGTTTGAATATGATGGAAAACTGAATCCAACTTTTGCGGAAGGCGCATTTCAGCTTCCAGTATCAAGCATAAGGGCATATATAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtataattttttaggaataactgaacctgaaattgctgtgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
gaataac putative branch site (score: 2)
ataattttttaggaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatgtgttcatgtgttggtataattttttaggaataactgaacctgaaattgctgtgataattctgtagCTCATGTTTAGCAAGTTTGAGTATGACGGAAAGCTGAACCCAACATTTACAGAAGGTTCATTTGAGCTCCCCTTTTCAAGTATTAGAGCATACATAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA