Sequence
atgc intronic sequence ATGC exonic sequence...catttccaatcacgaactatattacttattctcttaaaaaatatcacagttgcttctcattatattctgactatataattcactggctttttctttgcagAAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g18010.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g18010.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G455115_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------------------catttccaatcac---gaactatattacttattctcttaaaaaatatcacagttgcttctcattatatt-----ctgactata--taattcactg-gctttttctttgcagAAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
|||||| | | |||| || | || | || || | | | | | | || ||| || ||||| | | | |||| |||||||| |||| ||||||||||||| |||||||||||||||| |||||||||||| |||||||||||||| | ||| | |||||||| ||| || |
gtatgaagaacactttctgttgtgtggtaactatctgtttatggttaccttctattgcgctgtaatatttttccatttgctgtaggtgatatggtttctactgtctaagttcattttaatggttacatgatgagtttgctgctgctcattgctaatttatttcaccaaaactttacagAAGATCTCATTTGTTGTGAGAGATGCTCTGATCAATGTTGGTCCTCTGAAAGATTTTGCATATGGTTTAAGAACTAATTCTGATCCCAACGCAGCAGGCA
upper sequence: LOC_Os04g18010.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------catttccaatcacgaactatattacttattctcttaaaaaatatcacagttgcttctcattatattctgactata-taattcactggctttttctttgcagAAGATATCATAC------ATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
||| | ||| | | | || | |||| | | | | | || ||| || || ||| | || || | | | | | | ||||| | ||| ||| | | ||||| ||| ||||||| ||||||||||| |||||||||| ||||||||||||||| ||||| ||| | ||||| | |
gtagtgtctcgatatggatagaggaaaagtctcaggagattaagtgggcatttaacatcttttatttgtttatagacacaatccttcttgaattttctgt-ggtattttctgaaatcctttgacatattaaacttactgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAATGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG---
upper sequence: LOC_Os04g18010.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 11
----------------------------------catttccaatcacgaacta-tattacttattctct--taaaaaatatcacagttgcttctcat----tatattctgactatataattcactggctttttctttgcagAAGA---TATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
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gtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatttgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG---Mapped 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|29674862|gb|CB671137.1|CB671137EST: AACTTTCCTTTCACAATATCATTGCACCAAACAGTTTAGAATCAGCACAG AAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAA
genomic: AACTTTCCTTTCAGAATATCATTGCACCAAACAGTTTAGAATCAGCACAGgtctgagtat ... ttctttgcagAAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagttgcttctcattatattctgactatataattcactggctttttctttgcagAAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
ttctgac putative branch site (score: 2)
ctggctttttcttt putative PPT
attatattctgactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttccaatcacgaactatattacttattctcttaaaaaatatcacagttgcttctcattatattctgactatataattcactggctttttctttgcagAAGATATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcactg