Sequence
atgc intronic sequence ATGC exonic sequence...ttggaaatgtagaccaaacgcttattttataaagaaaattattcacaatccatcttgattaatgaatgataatatataaaaaaaactatttttggttcagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGACTTCATCTTTACATGGAACTGATTCCCTCCTATCTATTGTCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10280.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G036123_T01 (Zea mays), 3'ss of exon 4
ttggaaatgtagaccaaacgcttat-tttat--aaagaaaattattcacaatc-catcttgattaatgaatgataatatataaaaaaa-actatttttggtt-cagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGACTTCATCTTTACATGGAACTGATTCCCTCCTATCTATTGTCCAG
|| ||||| | | ||| ||||| |||| || ||||| | | | | | | || | |||| | | || | ||| || || || ||||||||||||||||||||||| || | || ||||| ||||| ||||| | ||||||| | || ||| ||||||||||||||||||||| ||
------ctgctgaccagattcgtatatttatttaaagtttatggaacacaaacacctaataaattttggtttttaattaaggataacacacttttgtttattgcagGGATGGTGGCTTCATTGACTCCTCTTCCTGTAATCGGAGTTCCCATTAAGACTTCAACACTATCAGGATTTGATTCCCTCCTATCTATTGTGCAA
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G133121_T02 (Zea mays), 3'ss of exon 12
ttggaaatgtagaccaaacgcttat-tttat--aaagaaaattattcacaatc-catcttgattaatgaatgataatatataaaaaaa-actatttttggtt-cagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGACTTCATCTTTACATGGAACTGATTCCCTCCTATCTATTGTCCAG
| ||||| | | ||| ||||| |||| || ||||| | | | | | | || | |||| | | || | ||| || || || ||||||||||||||||||||||| || | || ||||| ||||| ||||| | ||||||| | || ||| ||||||||||||||||||||| ||
------ccgctgaccagattcgtatatttatttaaagtttatggaacacaaacacctaataaattttggtttttaattaaggataacacacttttgtttattgcagGGATGGTGGCTTCATTGACTCCTCTTCCTGTAATCGGAGTTCCCATTAAGACTTCAACACTATCAGGATTTGATTCCCTCCTATCTATTGTGCAAMapped 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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatccatcttgattaatgaatgataatatataaaaaaaactatttttggttcagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGACTTCATCTTTACATGGAACTGATTCCCTCCTATCTATTGTCCAG
gattaat putative branch site (score: 3)
ctattttt putative PPT
ttgattaatgaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggaaatgtagaccaaacgcttattttataaagaaaattattcacaatccatcttgattaatgaatgataatatataaaaaaaactatttttggttcagGGATGGTGGCTTCATTGACTTCTGTCCCAGTAATAGGAGTACCCATCATGACTTCATCTTTACATGGAACTGATTCCCTCCTATCTATTGTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA