Sequence
atgc intronic sequence ATGC exonic sequence...gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g07830.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
----------------------------------------------gttctaaaagcttgccaagg----aaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
||| | ||| | | || || || | | || | || | | | | || || | | ||| ||||| |||| ||||||||||||||||| ||||||||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaattt------cttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtact-atgtaatttgatcattatgt-gcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
|| | | || | | | | | ||||| || | | | | || | |||| | || | | | | | ||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||
--atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 6
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgc-cataatggt--actatgtaatttg-atcatta--tgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
| || | | || || || | | | || ||||| || | ||| || || | | | | | ||| || ||| | | |||||||||||||||||| || || ||||| || || || ||||||||||||||| ||||||| ||||| ||||| |||||||||||||||||
----tgcaacatcccttagataatgagctttgataacagttattgtaagatc--aatgcatatggcagtttaatttatgacttgtattatttcctttctctcttagTTTGACCCAGTAAAGCTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATTGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 7
-gttctaa----aagcttgccaaggaaaagatcacatttgaacatttctgtaatatttta-gtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
||||| || | | | | || | |||| || || | | || || || | ||| | ||| | | | |||| ||||||| | | || | || || || || ||||||||||||| ||| ||| ||||||||||||| |||||||| || |||||
acttctagctgcaaattagttactatagtcattagttttgtgtatacttgcagttgaatacaaatcaatatattgttatat--tttccttttcctatgcc----agTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 5
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatatttt-agtgccataatggtac-tatgtaatttgatcattatgtgcctct--tagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
|| |||| || | | | | | | |||| ||| || ||| ||| ||| || ||| | || || | | | ||| | ||||||| | | || | || || || || ||||||||||||| ||| ||| ||||||| ||||| |||||||| || |||||
--acttctagct-gctattattgttactatagtc-attatttttgtcttactttcagttgaatacaaataaatatattgttatattttccttttcctatgccagTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcc----tcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
|| | | || || |||| | || | || || || | | || | | | ||| || | | || |||| | ||| ||||||| | | ||| ||| ||| ||||||||||||||||| |||||||| || |||||||| ||||| ||||| ||||| |||||
-cattacacgtcagcaaatgaaa--cttgtggttaag-ataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 8
---gttctaaaagcttgccaaggaaaagat-cacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
||||| || || | |||| || | | | || | | | ||| | ||| || | | || ||| || | | | ||||||||||| |||||| | ||||||||||| || ||||| ||||||||||| ||| |||| ||||| || ||||||||||| |||||
ttagttctttgagaaaataaatatatagatacagaatcaatcaatattacc-ttctttgttaatata-cattaatgtcta--ttgctcttgtgctttttgctagTTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGMapped 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|33678061|gb|CF306300.1|CF306300EST: GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAG TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
genomic: GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAGgtacaatcta ... tgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
atttgat putative branch site (score: 5)
tgcctctt putative PPT
taatttgatcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG