Sequence
atgc intronic sequence ATGC exonic sequence...gcatcctaataatttcgtagttttccattattcttgctttgtatttttttactgatgattttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G406177_T01 (Zea mays), 3'ss of exon 5
-------gcatcctaataatttc------gtagttttccat-tattcttgctttgtatttttttact---gatg----attttagtgaaagacttaccattcatcgtgtta----aatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
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gtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcctgtattttaattgttaacttttaataaatgaatttatgatgaatctgtagAATCTACTTGATGGGCCAATCAGCAGGAGCACATATCGCGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAAT
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G325504_T01 (Zea mays), 3'ss of exon 2
---------------------------gcatcctaataatttcg--tagttttccattattcttgctttgtatttttttactgatgatt-ttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
| || || || | | | || | || | |||| || | | | ||||| ||| | | | | | | || | |||| || || | ||||| |||||||||||||||||||||||||||| || ||| |||| || || ||||| ||| ||||||| ||||||| | | | |||| |
gtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcctgtattt--tgattgttaatttttaataaatgaat--ttatgatgaatc-tgtagAACCTACTTGATGGGTCAATCAGCAGGAGCACATATCGTGGCCTGCACTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAAT
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G437845_T01 (Zea mays), 3'ss of exon 6
---------------------gcatcctaataat----ttcgtagttttccatt----attcttgctttgtatttttt-tactgatgattttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
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gtaagtgatactttgacatttgtttgcaagtagtagtacttatagttgttcgttgagcatctctactttagatcctgtattttgattgttaacttttaataaatga-atttatgatg----aatctgtagAATCTACTTGATGGGTCAATCAGCAGGAGCACATATCGTGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAAT
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G854930_T01 (Zea mays), 3'ss of exon 8
---------------------------gcatcctaataatttcg--tagttttccattattcttgctttgtatttttttactgatgatt-ttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
| || || || | | | || | || | |||| || || | | ||||| ||| | | | | | || | ||||| | || || ||||| ||||||||||||||||||||||||||||| || |||||||| || || ||||| ||| ||||||| ||||||| | | | |||| |
gtaagtgatactttgacatttgtttgcaagtagtagtacttacagttgttctttgagcatctctactttagatcttgtattt--tgattgttaacttttaataaatgaat--ttatgatgaatcc-gtagAATCTACTTGATGGGTCAATCAGCAGGAGCACATATCGCGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAAT
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G427351_T01 (Zea mays), 3'ss of exon 7
---------------------------gcatcctaataatttcg--tagttttccattattcttgctttg-----tatttttttactgatga-ttttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
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gtaagtgatactttgacatttgtttgcaagtagtagtacttacggttgttctttgagcatctctactttagatcctatattttgattgttaacttttaataaatgaatt---------tatgatgaatc-tgtagAATCTACTTGATGGGTCAATCAGCAGGAGCACATATCGCGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGGATMapped 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|66926863|gb|CX113711.1|CX113711EST: ATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCA GATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCT
genomic: ATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAATCAgtaagtgata ... aatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttactgatgattttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
gacttac putative branch site (score: 2)
atgatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatcctaataatttcgtagttttccattattcttgctttgtatttttttactgatgattttagtgaaagacttaccattcatcgtgttaaatcctgcagGATATACTTAATGGGTCAATCAGCAGGAGCACATATCGCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
gcatcct
- - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca