Sequence
atgc intronic sequence ATGC exonic sequencegtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g37710.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G466549_T01 (Zea mays), 3'ss of exon 2
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaag-acatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaat---gctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG----------------------------------------------------
| ||| | ||| || || | | | ||||| |||| || | | | || ||| | || |||| |||| | | | | ||||||||||||||| || | ||| |||||||||||||||||||| ||| ||||
--------------------------------------------------------------------------------------------ctgatgccaccttgaagtacctgcatgccaattattactgtagaaaatcaatagtgtttccagg--tccgggctttagtaatagtgaatagggtgtttgcagGCAGTTAATCTCAGAAGTACAGAAGTTTCAAGCATTCCACGCATAAAGGTGAGCAGAAAAGAAATTCTACACTCACTGTGTCACAACTTTGAATTTTGGG
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G053298_T02 (Zea mays), 3'ss of exon 2
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaag-acatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaat---gctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG----------------------------------------------------
| ||| | ||| || || | | | ||||| |||| |||| | | || ||| | || |||| |||| | | | ||||||||||||||||| || | ||| |||||||||||||||||||| ||| ||||
--------------------------------------------------------------------------------------------ctgatgccaccttgaagtacctgcatgccaattattactgtagaaagtcaatagtgtttccagg--tccgggctttactaatagtgaacagggtctttgcagGCAGTTAATCTCAGAAGTACAGAAGTTTCAAGCATTCCACGCATAAAGGTGAGCAGAAAAGAAATTCTACACTCACTGTGTCACAGCTTTGAATTTTGGG
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G346037_T02 (Zea mays), 3'ss of exon 2
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaag-acatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaat---gctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG----------------------------------------------------
| ||| | ||| || || | | | ||||| |||| || | | | || ||| | || |||| |||| | | | | ||||||||||||||| || | ||| |||||||||||||||||||| ||| ||||
--------------------------------------------------------------------------------------------ctgatgccaccttgaagtacctgcatgccaattattactgtagaaaatcaatagtgtttccagg--tccgggctttactaatagtgaacagggtgtttgcagGCAGTTAATCTCAGAAGTACAGAAGTTTCAAGCATTCCACGCATAAAGGTGAGCAGAAAAGAAATTCTACACTCACTGTGTCACAACTTTGAATTTTGGG
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G053298_T01 (Zea mays), 3'ss of exon 2
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaag-acatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaat---gctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
| ||| | ||| || || | | | ||||| |||| |||| | | || ||| | || |||| |||| | | | ||||||||||||||||| || | ||| |||||||||||||||||||| ||| ||||
--------------------------------------------------------------------------------------------ctgatgccaccttgaagtacctgcatgccaattattactgtagaaagtcaatagtgtttccagg--tccgggctttactaatagtgaacagggtctttgcagGCAGTTAATCTCAGAAGTACAGAAGTTTCAAGCATTCCACGCATAAAG
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 1
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatg-atgactattgattacagtaggaagt-aactgaatattttaggcatatggactttctta--atgctaatgctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
| || || | || || || | ||| ||| |||| |||| || | || || | ||| | || ||| ||||| || ||| || | ||||||||||||||||| || | ||| ||||||||||| |||||||| ||| ||||
-------------------------------------------------------------------------------------------aaaaccggcttga--aatacctgcacgacaattatttactgtagaaaatcaatagagtgtttccag-atctgggctttcctattatgacaagggtctttgcagGCAGTTAATCTCAGAAGTACAGAAGTTTCGAGCATTCCACGCAAAAAGMapped 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|58606417|gb|CK034450.1|CK034450EST: AGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAG GCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCACAAAG
genomic: AGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcat ... ctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
tgctaat putative branch site (score: 2)
tgctcttt CT-rich tract
tgaatatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG