Sequence
atgc intronic sequence ATGC exonic sequence...aaattattgaagaaaattttgtcagaaagaaaaagagtgttgtgcacctatgtaaattagctgtctctgaaagaacaaaccctcatccttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g29220.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g29220.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
-----aaattattgaagaaaattttgtcagaaagaaaaagagtgttgtgcacctatgtaaattagctgtctctgaaagaacaaaccctcatc-cttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
|| || | | | ||||| | | || | | | | || | || | ||| ||| ||| | | ||| ||| ||||||| || |||||||| |||||||| ||||||||||| |||||||| |||||||| || ||||| ||||| ||||| ||||| || ||
tccctaagttctgttatgatcctttgttgttgttac------tattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
upper sequence: LOC_Os06g29220.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G01210.4 (Glycine max), 3'ss of exon 4
aaattattgaagaaaattttgtcagaaagaaaaagagtgttgtgcacctatgtaaattagctg-tctctgaaagaacaaaccctcatc-cttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
| | | || |||| | | | || | | | | ||| | | | | || ||| ||| | | ||| ||| ||||||| || |||||||| || ||||| ||||||||||| |||||||| |||||||| || ||||| ||||| ||||| ||||| || ||
--ttctgttatgatcctttttttttggttgttgttactattcctttttaagttgcaattgctaatttttttcatcctctttccaaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAACCAGCTCCAAAGGATCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGTACCAC
upper sequence: LOC_Os06g29220.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 4
-aaattattgaagaaaattttgtcagaaagaaa-aagagtgttgtgcacctatgtaaattagctgtctctgaaagaacaaaccctcatccttgt------gttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
||| || | | || || || || |||||| || | ||| | |||||| | | |||| | | || ||||| || |||| || || |||| || |||||||| || ||||| || |||||||| |||||||| || || |||||||||||||| ||||| || ||
gtaatgtttcagcacttttgagtttcttggatttgagtatgttgttcaatgtttctttttatgcagttttgaaagccaatgacttcattttaattttctgattttcagGTTACAGTGGGGATGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctatgtaaattagctgtctctgaaagaacaaaccctcatccttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
tccttgt CT-rich tract
tgtaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattattgaagaaaattttgtcagaaagaaaaagagtgttgtgcacctatgtaaattagctgtctctgaaagaacaaaccctcatccttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC
- - - - gaagaaa
- - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - -gtgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaaa