Sequence
atgc intronic sequence ATGC exonic sequence...acaatgcaacttagttgtttcagaattcacagttttgctgatcgccttctgattcaacgaaaacacccccaccaaatgaaatttcaatctatttgatcagGAGGACGTAGCTATTGCGGATGGCATACCGGAATTCCTCAAGAGGTCAATCCTGCTACAAACGTTCGGCGTACAGGGCACTCATGTGTGCCAGGAGGCGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01760.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G035377_T01 (Zea mays), 3'ss of exon 1
acaatgcaacttagttgttt-cagaattcacagttttgctgatcgccttctgattcaacgaaa----acacccccaccaaatgaaatttcaatctatttgatcagGAGGACGTAGCTATTGCGGATGGCATACCGGAATTCCTCAAGAGGTCAATCCTGCTACAAACGTTCGGCGTACAGGGCACTCATGTGTGCCAGGAGGCGG
| || ||| | | ||| ||| ||||||||| || || ||| || | || | | | ||| |||| ||| ||| ||| |||||||||||||||| || || || |||||||| || ||||| |||||||| ||||||||||| || || || || || ||| ||| || || ||||||| ||
-gtttagaatttaacaactgactgaacacac---cttgctgatcctctgcttatttaagggaaccctatttcactgaaaaaagaaagttccttct-tttaatcagGAGGACGTAGCCATCGCCGACGGCATACCAGAGTTCCTGAAGAGGTCCATCCTGCTACAGACATTTGGTGTCCAAGGCCATCACGTATGTCAGGAGGTGG
upper sequence: LOC_Os03g01760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G113245_T01 (Zea mays), 3'ss of exon 1
acaatgcaacttagttgtttcagaattcacagttttgctgatcgccttctgattcaacgaaaacacccccaccaaatgaaatttcaatc--tatttgatcagGAGGACGTAGCTATTGCGGATGGCATACCGGAATTCCTCAAGAGGTCAATCCTGCTACAAACGTTCGGCGTACAGGGCACTCATGTGTGCCAGGAGGCGG
| | | | || | || | | || | | ||| || ||| || | ||| || || ||| | ||| | ||| || ||||||| ||||| || || ||||| |||||||| ||||| |||||||| ||||||||||| || || || ||||||||| ||| || ||||||| ||
cttaggtcatctgatt-tcccaccctaggtatttggatttcccacctgcttatttaa-gggaacttcctattcactgaaaaagttaattattttttaattagGAGGATGTAGCCATCGCCGATGGTATACCGGAGTTCCTGAAGAGGTCCATCCTGCTACAGACATTTGGTGTACAGGGCCATCACACATGTCAGGAGGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctgattcaacgaaaacacccccaccaaatgaaatttcaatctatttgatcagGAGGACGTAGCTATTGCGGATGGCATACCGGAATTCCTCAAGAGGTCAATCCTGCTACAAACGTTCGGCGTACAGGGCACTCATGTGTGCCAGGAGGCGG
ttctgat putative branch site (score: 3)
tctattt putative PPT
aaatgaaatttcaatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaatgcaacttagttgtttcagaattcacagttttgctgatcgccttctgattcaacgaaaacacccccaccaaatgaaatttcaatctatttgatcagGAGGACGTAGCTATTGCGGATGGCATACCGGAATTCCTCAAGAGGTCAATCCTGCTACAAACGTTCGGCGTACAGGGCACTCATGTGTGCCAGGAGGCGG
-caatgca
- - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - ttgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - caacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaaa