Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttggttttcttgttacaatgtgtgtatgatgatgatgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g03400.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G382537_T01 (Zea mays), 3'ss of exon 4
gtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttggttttcttgttacaatgtgtgt-atgatgatgatgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
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gtgcgtgcgtgttccct-----------tgtcaaatactgggttcccctcggcgactatttactctaagcactggtgatgatatgcttactctagGCTATAAAGGATGGGGCTGATGCTGTGATCGCTGTTGGAGGTGATGGTACGCTTCATGAG
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G089860_T02 (Zea mays), 3'ss of exon 3
gtgtgtatgggcttcctatagctgccagtatccaat-tgttaatttccccttt-tggttttcttgttacaatgtgtgtatgatgatgatga-tgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
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--gtgcgtgcg-tgactgcgtgtccccttgtcaagtgtactaggttccacttggtaactatttaatctaagcactggtgatgtcctaattactgtagGCTATAAAGGATGGGGTTGATGCCGTGATAGCTGTTGGAGGTGATGGTACACTTCATGAG
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G47330.1 (Glycine max), 3'ss of exon 3
gtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttggttttcttgttacaatgtgtgtatgatgatgatg-atgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
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---------ggttagtttggagtgtttgagataagttggtt-ttatctcagctgattccaatgagttgttgaattgctgtccttgttctatgtaGGCTATAAGGGAGGGGGCTGATGCTGTCATTGCTGTTGGAGGAGATGGAACTCTTCATGA-
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G39010.1 (Glycine max), 3'ss of exon 3
gtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttggttttcttgttacaatgtgtgtatgatgatgatgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
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gtcagtttggagtgtttgagataagttggtttta--tgtcaattgcttccaatgagtt----gttaaatcgt---tgtccttgc-actatgtagGCTATAAGGGAGGGGGCTGATGCCGTCATTGCTGTTGGAGGTGATGGAACTCTTCATGAG
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gt-gtgtatgggct-tcctatagctgccagtatccaattgttaatttcccct-tttggttttcttgttacaatgtgtgtatgatgatgatgatgt-agGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
|| ||| | | | | ||| ||| ||| | | | | ||||||||| | | | | ||| | | || || | | ||||| ||| |||||| || ||||| || ||||| ||||| |||||||||||||||||||||
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0046g01770.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttg---gttttcttgttaca----atgtgtgtatgatgatg--atgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
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gtaggggttttgagccttagta-gtttgagtttgaaatttgaactcaattttaatttttaacactgtactttgaaagattgcttataattccttatattcatctgccaatcttatgatgcagGCCATACGGGAGGGTGCTGATGCCGTGATTGCAGTTGGAGGGGATGGAACTCTTCATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttccccttttggttttcttgttacaatgtgtgtatgatgatgatgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
tgttaat putative branch site (score: 3)
ttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtatgggcttcctatagctgccagtatccaattgttaatttccccttttggttttcttgttacaatgtgtgtatgatgatgatgatgtagGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA