Sequence
atgc intronic sequence ATGC exonic sequenceGAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g37710.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G346037_T01 (Zea mays), 5'ss of exon 5
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaa-----gaaatcttgttgtaagtatct--gaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
||||||| | ||||||||||| |||||||| ||||||||||||||||||||||||||| || | ||| | | | ||| || | | | |||| | | | | || || || | || | || |
------------------------------------------------GCAGAAGATAAACTTCACCTCTGAGCTCAACACCATTTGCAGTGCTCTCCAGgtatgaaacctcctcaatctcactgctcctgaaagttcagagaagtatatcgcaagtgtgttaggttaggagatcaaatcaccagcttagtgcaggaaag-------------------------------------------------------------------------------------------------
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G346037_T02 (Zea mays), 5'ss of exon 2
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaa-----gaaatcttgttgtaagtatct--gaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
|| ||| | |||| || | || ||||||||| |||||||||| | ||||||| | ||||||||||| |||||||| ||||||||||||||||||||||||||| || | ||| | | | ||| || | | | |||| | | | | || || || | || | || |
GAAGGGAAGCTACAACTGACTGGGCGTCATCGAGCTGATCATGACAAGGCAGAAGATAAACTTCACCTCTGAGCTCAACACCATTTGCAGTGCTCTCCAGgtatgaaacctcctcaatctcactgctcctgaaagttcagagaagtatatcgcaagtgtgttaggttaggagatcaaatcaccagcttagtgcaggaaag-------------------------------------------------------------------------------------------------
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G053298_T02 (Zea mays), 5'ss of exon 2
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaa-----gaaatcttgttgtaagtatct--gaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
|| ||| | |||| ||| | || ||||||||| |||||||||| | ||||||| | ||||||||||| |||||||| ||||||||||||||||||||||||||| || | ||| | | ||| || | | | |||| | | | | || || || | || | || |
GAAGGGAAGCTACAACTGCCTGGGCGTCATCGAGCTGATCATGACAAGGCAGAAGATAAACTTCACCTCTGAGCTCAACACCATTTGCAGTGCTCTCCAGgtatgaaacctcctcaatctcactgcccctgaaagttcagagaagtatatcgcaagtgtgttaggttaggagatcaaatcaccagcttagtgcaggaaag-------------------------------------------------------------------------------------------------
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G048582_T01 (Zea mays), 5'ss of exon 1
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgag-catcacttactctg-----aaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
|| | | ||| ||| | || || |||||| |||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||| ||| | ||| | | ||| |||||||| | ||| | | | | | | | || || ||| || | || | | |
GAAAAGAAGTTACAGTTGCCTGGGCGTTATCGAGCTGATCATGACAAAGCAGAAGCTCAACTTCACCTCTGAGCTCAACACCATCTGCAGTGCTCTACAGgtaggagacctcaatctcactgcccctgaaagttcagagaagtataccg--caaatgcgttaggttaggagatccactcaccagcttaggacatgtttagaa----------------------------------------------------------------------------------------------
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G466549_T02 (Zea mays), 5'ss of exon 2
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaa-----gaaatcttgttgtaagtatct--gaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
|| ||| | |||| ||| | || ||||||||| ||||||||| | ||||||| | ||||||||||| |||||||| ||||||||||||||||||||||||||| || | ||| | | ||| || | | | |||| | | | | || || || | || | || |
GAAGGGAAGCTACAACTGCCTGGGCGTCATCGAGCTGATCATGATAAGGCAGAAGATAAACTTCACCTCTGAGCTCAACACCATTTGCAGTGCTCTCCAGgtatgaaacctcctcaatctcactgcccctgaaagttcagagaagtatatcgcaagtgtgttaggttaggagatcaaatcaccagcttagtgcaggaaag-------------------------------------------------------------------------------------------------
upper sequence: LOC_Os09g37710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143566_T01 (Zea mays), 5'ss of exon 2
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaa-----gaaatcttgttgtaagtatct--gaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
|| ||| | |||| ||| |||| ||||||||| |||||||||| | ||||||| | ||||||||||| ||||||| ||||||||||||||||||||||||||| || | ||| | | ||| || | | | |||| | | | | || || || | | || | || |
GAAGGGAAGCTACAACTGCCTAGGCGTCATCGAGCTGATCATGACAAGGCAGAAGATAAACTTCACCTCTAAGCTCAACACCATTTGCAGTGCTCTCCAGgtatgaaacctcctcaatctcactgcccctgaaagttcagagaagtatatcgcaagtgtgttaggttaggagatcaaatcactagcttagtgcaggaaag-------------------------------------------------------------------------------------------------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|58606417|gb|CK034450.1|CK034450EST: AGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAG GCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCACAAAG
genomic: AGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcat ... ctctttgcagGCAGTTAACCTGACAAGCACAGAAGTTTCAAGCATTCCGCGCGCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGGGGGAACTACTCATGCTTAGGTGTCATCGAGTTGATCATGACCAAGCAGAAGCTCAACTTCACCTCCGAGCTCAATACCATTTGCAGTGCTCTCCAGgtatgagcatcacttactctgaaaagttcaaaaaagaaatcttgttgtaagtatctgaccaagaaataaacttggttgcacaagaaagagcacgtatggtttcaccaagacatgatgactattgattacagtaggaagtaactgaatattttaggcatatggactttcttaatgctaatgctctttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA