Sequence
atgc intronic sequence ATGC exonic sequenceCATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagaccaaattatgtgcatactggtacacttgtgttttgtcta...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10280.2 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G133121_T02 (Zea mays), 5'ss of exon 12
CATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagaccaaattatgtgcatact-ggtacacttgtgttttgtcta-------------
||||||||||||||| ||||||| ||||||| ||| ||||||| || || || ||||||||||||||||||||||| ||||| ||||| ||||||||||||| | ||| ||||| || | || ||| | || | || | || || |||| || | ||| ||||| | |||| || |
CATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCGGAGCAGCTCATTTACCAGgcaagtat----aaaattacacaaatatta-tgtttcaaagta---------aatttcaagtcatgttgcgtgcgtattaggtgcacttatattttatcgacattgaagtaatt
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G036123_T01 (Zea mays), 5'ss of exon 4
CATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagaccaaattatgtgcatact-ggtacacttgtgttttgtcta-------------
||||||||||||||| ||||||| ||||||| ||| ||||||| || || || ||||||||||||||||||||||| ||||| ||||| ||||||||||||| | |||| ||||| || | || ||| | || | || | || || |||| || | ||| ||||| | |||| || |
CATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCGGAGCAGCTCATTTACCAGgcaagtat----aaaaatacacaaatatta-tgtttcaaagta---------aatttcaagtcatgttgcgtgcgtattaggtgcacttatattttatcgacattgaagtaatt
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G05140.1 (Arabidopsis thaliana), 5'ss of exon 2
CATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagacc---aaattatgtgcatactggtacacttgtgttttgtcta
||||| || ||||||| |||||| |||||| || || | ||||| | | ||||| ||||||||||| ||||| || |||||||||||||| | || | | |||||||||| |||| | || || | || | || ||| | | | | || | | | | |
CATCGCACCCCAGAGATGATGTATACATATGCAACCTCAGCTCATAGTCGAGGCGTTCAAGTCATCATTGCAGGTGCTGGTGGTGCTGCTCACTTACCAGgtatgtctttaa---------catgcatgaactcatcttgtcacctcccagaagattgttactgtaaaacaaaggactttcttggaaattag-----------
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G37690.1 (Arabidopsis thaliana), 5'ss of exon 14
CATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagacc---aaattatgtgcatactggtacacttgtgttttgtcta
||||| || ||||||| |||||| |||||| || || | ||||| | | ||||| ||||||||||| ||||| || |||||||||||||| | || | | |||||| |||| | | || | || | || |||| ||| | || | | | | |
CATCGCACCCCAGAGATGATGTATACATATGCAACCTCAGCTCATAGTCGAGGCGTTCAAGTCATTATTGCAGGTGCTGGTGGTGCTGCTCACTTACCAGgtatgtctttaa-------------catgaactcatcttgtcccctcccacaagattgttactgtaaaataatggattttcttggaaattag-----------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|86853694|gb|CI330545.1|CI330545EST: CAGGTGGAGCGGCTCACTTACCAG GGATGGT-GCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGA
genomic: CAGGTGGAGCGGCTCACTTACCAGgcaagtgtga ... tttggttcagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTGGAGCGGCTCACTTACCAGgcaagtgtgacagaaaaaacacatgcatgaatgcatcataatacttcatattagttcaagaccaaattatgtgcatactggtacacttgtgttttgtcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG