Sequence
atgc intronic sequence ATGC exonic sequence...gcagcctgtttgcttgaagaatgaatctcttctactttcttgttcctttcaaaaattttttacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g43400.4 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 1
-------------------------------------gcagcctgtttg-cttgaagaatgaatctcttctactttcttgttcctttcaaaaattttttacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
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tgttaatgaacttattattattattattattattccaagatcataattggctttaattgctttcctcttctgatttgccttgctttcctt---ttggctatagACAGTGTGTTTCGAACAGATTCTTCTACAAGGCAGGTGTATGAAAAAGCAGCTAAGGAAGTTGCTCTTTCAGTTGTCGGTGGCATCAACT
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 1
-------------------gcagc-ctgtttgcttgaagaatgaatctcttctactttcttgttcct-------ttcaaaaattttt--------tacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
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ggtcatatatacacatgaagttgctccattggttttgttaatgaacttattgttataccaagatcataattggctttaattgctttccttttggctatagACAGTGTGTTTCGAACAAATTCTTCTACAAGGCAGGTGTATGAAAAAGCAGCTAAGGAAGTTGCTCTTTCAGTTGTCGGTGGCATCAACT
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gcagcctgtttgcttgaagaatga-atctcttctactttcttgttcctttcaaaaatttt--ttacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
||| | | || || ||| || |||||| || || ||| | | | ||| || ||| || || ||| | |||||||| |||| ||| |||| || |||| |||||| || ||||||||||| || ||||||||||| || || |
gttcccacaattttacatcattctgcaaaactctcagggcctcttct-gatttctgatatttcttctgtttattttttctgtgctattgctttggttctagACAGAGTATTTAGGTCTGATTCCACTACGAGGGAGGTATATGAGGCAGGAGCCAAGGAAGTTGCTCTTTCGGTTGTCAGTGGTATTAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcaaaaattttttacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
tcctgat putative branch site (score: 3)
ttcctctac CT-rich tract
aaaaattttttacaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcagcctgtttgcttgaagaatgaatctcttctactttcttgttcctttcaaaaattttttacagatagggtgtttggtcctgattcctctacaaggcagGTCTACGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtcctg