Sequence
atgc intronic sequence ATGC exonic sequence...ttgcccgaaagttgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g13110.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
ttgcccgaaagttgtgt-caaatgacttgagcattgcttttttcacaaggtggttttgatatcatgata----tgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
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----tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatca-gtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
ttgcccgaaagttgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgcatcttaatta--catgtgtttcttgttt--cagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
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----cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 1
ttgcccgaaagttgtgtcaaatgac--ttgagcattgcttttttcacaaggtggttttga----tatcatgatatgcatcttaattacatgtgtttcttgttt-cagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
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------gctgactttgttaggtcataattgttcgc-atttttctcacaggttaaaattgagttattttctaactagtttgtctattttccaactgtcctatctacagTTGATATCATATCAGCTATTGAGTTTGATAAAACTGGGGACCATCTTGCTACTGGAGATCGTGGGGGTCGGGTGGTTTTATTTAACAGAACTGATACGAG
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 1
---ttgcccgaaagt-tgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
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actttgttgggaagtgtggtttttttagtgtatgtattgttggatgaaatctgcgagattcctattttc-tttgcttctaatgtg---gtgtttcattttgcagTTGATATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAA
upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 1
ttgcccgaaagttgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgc---atcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
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--gccc-atgtttgtttatcttggcgagggcgatagtatttgctgttggggattcatatatgcttgtttctcaaatataaattgttttgttgtatgaatgcagTTGACATCATCTCTGCTATTGAGTTTGATAAAACTGGAGAGCATTTGGCGACTGGAGACCGAGGAGGACGAGTTGTGCTGTTTGAGAGGACGGATGGCAGMapped 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|9864945|gb|AU100695.1|AU100695EST: GTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAG TTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCA
genomic: GTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaacgc ... cttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtggttttgatatcatgatatgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
tcttaat putative branch site (score: 3)
tttcttgtttc putative PPT
atcttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcccgaaagttgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - -tgctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt