Sequence
atgc intronic sequence ATGC exonic sequence...aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g22400.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g22400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G849959_T02 (Zea mays), 3'ss of exon 4
-----------aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA-------
|| | | ||| ||| | | || ||| | | || | | |||| | ||| | | ||||| ||||||| ||| |||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||| |||| |||||| ||||| || ||||| || ||||||
atggacttctgccttgcatgtatctgccttcgtttattgttcatggatttttttttgccta-tgaatgttgatccttactgacttcctgaat-gtta---------ctcagCTTGCTTGTGGAAAAAATGGTTATGATTACAAATCTGTTAAAAGATGGACCTCCCAAAGGAAGTTGGGATATGAACTCATTGAATGCGATAAAGTAATGT
upper sequence: LOC_Os03g22400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G849959_T01 (Zea mays), 3'ss of exon 4
-----------aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
|| | | ||| ||| | | || ||| | | || | | |||| | ||| | | ||||| ||||||| ||| |||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||| |||| |||||| ||||| || ||||| || ||||||
atggacttctgccttgcatgtatctgccttcgtttattgttcatggatttttttttgccta-tgaatgttgatccttactgacttcctgaat-gtta---------ctcagCTTGCTTGTGGAAAAAATGGTTATGATTACAAATCTGTTAAAAGATGGACCTCCCAAAGGAAGTTGGGATATGAACTCATTGAATGCGATAAA
upper sequence: LOC_Os03g22400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0020g01220.t01 (Vitis vinifera), 3'ss of exon 4
-aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
|||| || ||| || | | || || || | | | || | | || ||| || || | | ||| | | || | ||| ||||||||| |||||||||| |||||||||||| | |||| |||||| || |||| ||| ||||| |||
acatttacttatctcaggtttctgtttggtctttggtttctataatttaagtttggtggtg-ttgatatcatgatcctcttttcctgaatgatgttcccagTTAATAAGTGGGAGGAATTCCTATGACTATAAATCTGTTAGAAGATGGACTACGCAAAGGAAGTTGGGATACAGCCTTAGTGAATGTGACAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
taatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattttaccatttcattttcatttgtgaatgctgaattgctgatcaccaagtaaatgctaatcttcattgactccctgaattgttggtcgtttggttcagCTTGCTTGCGGAAAAAATGGCTATGACTACAAATCTGTTAAAAGATGGACTACCCGCAGGAGGTTGGGTTATGAGCTTATTGAGTGTGATAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT