Sequence
atgc intronic sequence ATGC exonic sequencegtgacaatgcctccaaaatcagatgctgccgcatgcatgccgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g49986.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G33620.1 (Glycine max), 3'ss of exon 2
------gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgccactcgatccaaaatctcatggtgtttt-tgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
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cctagtatggaccttttgttggaatcatttttttaataataataattgtgattcctttactaattac-tgatatcttgtatttttttcctccct-tatgcagATGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACTGATAATGAGATCAAGAATCACTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATT
upper sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
-gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgcc--actcgatccaaaatctcatgg--tgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT-
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agttatttttcctatgtaaacat-tcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
upper sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 2
---gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtac--agATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
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tttctttcattttcgcgtgttttcttttgtaatcaatactatatactatttaatactactatatatcattttactaattgtcattttcctttttactcagATGGTCCAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAACCATTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGCATT
upper sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G66230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
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-----------------gttaacaaacgtttcttacttgt-gctttaagtttcgatatgttctgtt-tttgagattttgttttttgtatgtaaagGTGGTCAAAGATAGCTTCTCATTTACCAGGAAGAACAGACAACGAAATCAAGAATCATTGGAACACTCACATCAAGAAGAAGTTGAGGAAAATGGGGATT
upper sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 2
----gtgacaatgcctccaaaatcagatgctgc-cgcatgcatgccgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
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ttccttttttttgtccctgaaattaattccaaaacatatccatgtgaaattcttcttcaattttaatttatatgtttgttttttcaacgtggatttgcagATGGTCCAAGATTGCTTCTCATCTACCAGGAAGAACCGATAACGAAATCAAGAACCATTGGAATACCCACATCAAGAAAAAACTTAAAAAGATGGGTATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|15072264|gb|C74411.2|C74411EST: GAAGAGGAGGAGAAGCTGGTCATTGACCTCCACGAGCAGCTCGGCAACAG ATGGTCCAAGATTGCGGCACGGCTTCCCCGGGAAGACGGACAACGAGATCA
genomic: GAAGAGGAGGAGAAGCTGGTCATTGACCTCCACGAGCAGCTCGGCAACAGgtgacaatgc ... gtgcgtacagATGGTCCAAGATTGCGGCACGGCT-CCCCGGGAGGACGGACAACGAGATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
aaaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgccactcgatccaaaatctcatggtgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG