Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatctgagaatttgcataatttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g04210.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 4
----gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatctgagaatttgcataatttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
|| |||| || || ||| || || | || || | || || ||||| ||| | ||| || || ||||| || ||||||||| ||| |||||| |||| |||| ||| |||| | ||||| || ||||||||||||||||| ||| |||||| |||||||||
gtaagtgagtcg-atcgatttttctttctttctttcccgcctcttcaagtccgt-----gtgatgtggtctga--attcctctg--ttggtc-tctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG
upper sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 5
gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatc-tgagaatttgcata-----atttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
|| | | | | || | | | | | | | | | | | || | | ||| || | |||| | |||||||||||| ||||| || ||||| ||||| || ||||| |||| | ||| |||| || ||||| |||||||| || || ||||| |||||||||| ||
-caatttgtgttgatattttaatttgactaaattctttggacagatgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
upper sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 7
gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatc-tgagaatttgcata-----atttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
| | | | | | | | | | | | | | | | | || | | | ||| || | |||| | |||||||||||| ||||| || ||||| ||||| || ||||| |||| | ||||||||| || ||||| |||||||| || || ||||| |||||||||| ||
-ccatttgtgttgatattgtaaattgactaaattctattgacagaggttctgtttctgttttgcttattacaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCAGTGGAAGGACCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaaagaacagacagcaatctgatctgagaatttgcataatttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
aatttgcataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatctgagaatttgcataatttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT