Sequence
atgc intronic sequence ATGC exonic sequencegtgatatactattcctttattcatcgtttagcatcttcctccgattttatcatttaataaataattattattgcatctaccctttcctggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49730.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G457881_T04 (Zea mays), 3'ss of exon 5
gtgatatactattcctttattcatcgtttagcatcttcctccgattttatcatttaataaataattattat-----tgcatctaccctttcctggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
||| ||| || ||||| | |||| | || |||||| || | | | | |||| | ||| |||||| | |||||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||||| |||| |||| |||| |||
------------------atttatc---tattatctttaccagattagagcaattaatatatcaccaccttctctattcatccattttttttgggtatattcagttgtgtaccaaatgcagTTTTGATATTTGATGGTAGGACAGCATATGTTCGTGCATTGCAACCGATAAATAAAGATGAAGAG
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G457881_T03 (Zea mays), 3'ss of exon 6
-----gtgatatactattcctt---tattcatc-gtttagcatcttcctccgattttatcatttaataaataattattat-----tgcatctaccctttcctggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
|| || |||||| | ||||||| | || ||||| | |||| | || |||||| || | | | | |||| | ||| |||||| | |||||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||||| |||| |||| |||| |||
gtcgtatgctaaactattagctatatattcatttatctattatctttaccagattagagcaattaatatatcaccaccttctctattcatccattttttttgggtatattcagTTGTGTACCAAATGCAGTTTTGATATTTGATGGTAGGACAGCATATGTTCGTGCATTGCAACCGATAAATAAAGATGAAGAG
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G399311_T01 (Zea mays), 3'ss of exon 5
gtgatatactattcctttattcatc-gtttagcatcttcctccgattttatcatttaataaataattattattgc-atctaccctttcct--ggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
| ||||| | ||||| | | || ||||| | |||| | || |||||| || || | | | || | || || | |||||| | |||||||||||||||||||||||||||||||| ||| ||||| |||||||||||||||||||||| ||| ||| |||| |||
---aactactagctatatattcgtttatctattatctttaccagattagagcaattaatatatcatcaccttctctattcatccattttttgggtatattcagTTGTGTACCAAATGCAGTTTTGATATTTGATGGTAGGACAACATATGTTCGTGCATTGCAACCGATAGACAAAGATGAAGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58682029|gb|CK070716.1|CK070716EST: AGGTCCCTTGGGACTGGACTATACCCTGTTTTATCTATTATTAACCACAG TTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCG
genomic: AGGCCCCTTGGGACTGGACTATACCCTGTTTTATCTATTATTAACCACAGgtgatatact ... gtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcatttaataaataattattattgcatctaccctttcctggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
atttaat putative branch site (score: 4)
tcatttaataaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatatactattcctttattcatcgtttagcatcttcctccgattttatcatttaataaataattattattgcatctaccctttcctggtatacttagTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG