Sequence
atgc intronic sequence ATGC exonic sequencegtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g50620.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 6
gtttggactcttggatcactaac-caaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
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--------gtttgaatcatgaatataaattttcttgtcaatga--agatatattgaaccaaaa---------accaagcctgagtacgtttgttttttcatgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 8
gtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
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--------gtttgaatca-tgaatagaaattttcttgacaatgaatatatattgaaccaaaacccaa--gcccgagtac-------ggttattttttcatgatccagTTTGTCAGCGATGTAACAAAATACATTAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 6
gtttggactcttggatcactaaccaaatat-atttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttg-agttttgttttgcttggtta-agTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
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agaaaaaatctggtatttagtatgaattttcatctgacttttggaagttatatgcggtgccaatgtcc---------tctaatttgtagttttgttgt-cgggcttatagTTTGTCTCAGATGTCACCAAATACATTAGTGGCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTGMapped 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|86530562|gb|CI170768.1|CI170768EST: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST:
gi|58611474|gb|CK039186.1|CK039186EST: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG TTTGTTAGTGATGTGACAAAATACATC
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATC
EST:
gi|426369|gb|D22232.1|D22232EST: TGAAACGGAAAAATTTCAACGNTTGTGCTGTGTACCTTCTTGATTCACAG TTTGTTAGTGATGT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
gtcttac putative branch site (score: 3)
ttttgctt putative PPT
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG