Sequence
atgc intronic sequence ATGC exonic sequence...cttcattgtgcatttcactagttgctgatctttaacagttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g36740.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 5
--------------------------------------cttcattgtgcatttcactagtt--gctgatctttaacagttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
|| ||| | || ||| | | || | ||| |||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
gttagtgattaatacattgtatatctcctgtgtttttttgtcgatgtaaagttaactgactctgttggtatttgacagCTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG
upper sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 3'ss of exon 2
---------------------------------------cttcattgtgcatttcactagtt--gctgatctttaacagttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
| ||| | || | | | |||| ||||| ||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
gttagcgatcgatacattgcatatctcctgtgttttttttggcgatgtaaagttaattgactctgctggtctttggcagCTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG
upper sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------cttcattgtgcatttcactagttgctgatctttaac--agttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
| | | || | | ||||| ||| || | | || | | |||||||||||| | || ||||||||||||||||||||||| || ||||| | || || | |||||| ||||||
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG
upper sequence: LOC_Os02g36740.4 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------cttcattgtgcatttcactagttgctgatctttaacagttgtttcttt----tgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
| || |||| | | || | | | ||| | || | | || ||||| ||| | || || || || ||||||||||||||||||||||| | ||||||| |||||||||||||
gtacgtacatctctcttactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgttttcttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
tatatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcattgtgcatttcactagttgctgatctttaacagttgtttcttttgagggctgctggatttttgctgccatgctatatcatggcttgggctattagTATCATGCAACGTCAAAGACAAAGACAG
- - - -gtgcatt
- - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggct