Sequence
atgc intronic sequence ATGC exonic sequence...aaactcaaaatctcttatattataggatagagggattactatatgattgcgctctgttgcataaaaattatgaatcgaattaccgtgtttgaacttgcagGTGACCAAGGATGGGTACCCGGTCATCTTCCACGACGACTTCATCTTCACCGAACAAGAC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g32320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g32320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G829946_T04 (Zea mays), 3'ss of exon 1
aaactcaaaatctcttatattataggatagagggattactatatgattgcgctctgttgcataaaaattatgaatcgaattaccgtgtttgaacttgcagGTGACCAAGGATGGGTACCCGGTCATCTTCCACGACGACTTCATCTTCACCGAACAAGAC
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acgcggcaactccctgcgattaagccctccttatctcactcagtctttgcaactcagcgagcgagcaagcaagcgctaaccatggccatgaatcttgcagGTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGAC
upper sequence: LOC_Os04g32320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G829946_T02 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------aaactcaaaatctcttatattataggatagagggattactatatgattgcgctctgttgcataaaaattatgaatcgaattaccgtgtttgaacttgcagGTGACCAAGGATGGGTACCCGGTCATCTTCCACGACGACTTCATCTTCACCGAACAAGAC
| | || || || |||| | | ||| | |||| | | | | || | | | | |||||||||||||| ||| || | ||| ||||||||||| ||| ||||||||| ||| ||||||||
gtgattccatacgccaaacgcatgaccgatcgatcaagttggaataaaataaacgcatgccggctgcgctgattgcgtacgcggcaactccctgcgattaagccctccttatctcactcagtctttgcaactcagcgagcgagcaagcaagcgctaaccatggccatgaatcttgcagGTGACCAGGGACGGCTGCCCTGTCATCTTCCATGACAACTTCATCTACACGCAACAAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcgctctgttgcataaaaattatgaatcgaattaccgtgtttgaacttgcagGTGACCAAGGATGGGTACCCGGTCATCTTCCACGACGACTTCATCTTCACCGAACAAGAC
ataaaaattatgaatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaactcaaaatctcttatattataggatagagggattactatatgattgcgctctgttgcataaaaattatgaatcgaattaccgtgtttgaacttgcagGTGACCAAGGATGGGTACCCGGTCATCTTCCACGACGACTTCATCTTCACCGAACAAGAC
- -ctcaaaa
- - - - - - - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa