Sequence
atgc intronic sequence ATGC exonic sequence...ccattttagggtgttgatgtggatcaacaagagatgaattttgaagttcctgtaagttggacatatctactggttccttactgctcttctattttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g51480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g51480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025409_T01 (Zea mays), 3'ss of exon 1
ccattttagggtgttgatgtggatcaacaagagatgaattttgaagttcctgtaagttggacatat----ctactggttccttactgctcttc-tattttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
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-catac-aggaaatgcctgcacctaaacatgagactcacc---aaatttcagcatgatggatttttttttctttcggttcattccatatcttcatgttctgctagGTATTCAGATGGATGCAGAAACAACGGTGGTATGTTGCTGACAACGGCATCTACTCCAAGTTAATATCTGTGATGGGAAGGAAAGGGCAGATACGGATGG
upper sequence: LOC_Os02g51480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G14860.1 (Glycine max), 3'ss of exon 1
ccattttagggtgttgatgtggatcaacaagagatgaattttgaagttcctgtaagttggacatatctactggttcc-ttactgctcttctattttgct-agGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
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-cattat-gcaagaacatagtaatctgcattagataaaatacgggaatatgattgatcgtgtcaatagttaaatttagttgtgaattttgtttgacattcagGTTTTCAGATGGATGCAAAAACAACGATGGTATATTGCTGATAATGGGATTTACTCAAAACTGATATCCGTTATGGGAAAGAAAGGGCAAACCAGAATGG
upper sequence: LOC_Os02g51480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G31640.1 (Glycine max), 3'ss of exon 1
ccattttagggtgttgatgtggatcaac---aagagatgaattttgaagttcctgtaagttggacatatctactggttccttactgctc-ttctattttgc---tagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
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------gaacatagtaatatgcattagttaaaataggggagcatgaatgatgatgtcaat-ggttatctctgtctcattgtagttgtgaattttgtttggcattcagGTTTTTAGATGGATGCAAAAACAACGATGGTATATTGCTGATAATGGGATTTACTCAAAACTCATATCAGTTATGGGGAAAAAAGGGCAAACCAGAATGG
upper sequence: LOC_Os02g51480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv07s0031g01360.t01 (Vitis vinifera), 3'ss of exon 1
-ccattttagggtgttgatg---tggatcaacaagagatgaattttgaagttcctgtaagttggacatatctactggttccttactgctcttctattttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
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ggagtgctaagctgcttataacatgagtcatgtttgtgtccatgttggcagccat-tagattgaatgaaaaggttgcttcatttaca-tgtcctacatt--cagGTATTCAGATGGATGCAGAAACAGCGCTGGTATATTGCTGATAATGGTGTTTACTCAAAGTTAATATCAGTTATGGGGAAGAAAGGCCAAACCCGGATGGMapped 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|11442802|gb|BF430701.1|BF430701EST: TCCTCTTCGAGGAGCTCGGCCGCCGCGACGGCTGGCTCCAGTGTCTCGAG GTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATA
genomic: TCCTCTTCGAGGAGCTCGGCCGCCGCGACGGCTGGCTCCAGTGTCTCGAGgtgagcatgg ... attttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcctgtaagttggacatatctactggttccttactgctcttctattttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
tccttac putative branch site (score: 2)
ttccttactgctcttc CT-rich tract
ttctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattttagggtgttgatgtggatcaacaagagatgaattttgaagttcctgtaagttggacatatctactggttccttactgctcttctattttgctagGTTTTCAGATGGATGCAGAAACAAAGGTGGTATGTTGCTGATAACGGCATATATTCGAAGCTGATATCTGTGATGGGAAGGAAAGGCCAGATACGGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - gttgatg
- - - - - - - - - - - - caacaag
- - - - - - - - - - - - - - - - gatgaat
- - - - - - - - - - - - - - - - - - - - - - -gttcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactgg