Sequence
atgc intronic sequence ATGC exonic sequencegtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatagacatctcacttcatacgttcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69920.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G423456_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------gtttttagtcttacatctcacttccttctgcttgcacacatccttct----gagttaggata-gacatctcact---tcatacgttc------ttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------gtttttagtcttacatctcacttccttctgcttgcacacatccttct----gagttaggata-gacatctcact---tcatacgttc------ttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG------------------------------------------------
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gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G471529_T01 (Zea mays), 3'ss of exon 5
------------------------------------gtttttagtcttacatctcacttccttctgcttgcacacatccttctgag--ttaggatagacatctcacttcatacgttct-tttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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gtgattagttcgctgcaaactatgcgtgtttgtgttactgtttctcttggaggccaaaggcttgttcttttctctctttttcgagggaccaaaaatggcaccttattaattcaatgctgtttttgcatgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTCCTAG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G11060.2 (Glycine max), 3'ss of exon 6
gtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatagacatctcacttcatacgt-tcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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-----gtatggaacttttttttaaaatttatttgttgaacttattttggcttaactcatactgatcatgtgggctttatcaattgtaaccgcagTTTCTTGCTACTGTTTCCCATGAGATCAGAACACCAATGAATGGTGTTTTGG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G28070.1 (Glycine max), 3'ss of exon 5
gtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatagacatctcacttcatacgt-tcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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gtatgtaactttatttatttatttatttattttgaac---ttgttttggcttaactcacactgatcatgtgggctttatcaattgtaaccacagTTTCTTGCTACTGTTTCCCATGAAATCAGAACACCAATGAATGGTGTTTTAG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtttttagtcttacatctcacttccttctgct-tgcacacatccttctgagttaggatagacatctcacttcatacgttcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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gtaaatacatcatcct-cagttgataaatttccacagcatattaaactttctatgacagagagaagagttgtaatctaactttttttta----tgcagTTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 3'ss of exon 5
gtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatagacatctcacttcatacgttcttttccgct-tgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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gtatttgatgcttttagtca--acttactgaaagcttgttttggcttaacctatcacagtgatttagttctaatgaaagttcaacgttctatagTTCCTTGCCACTGTTTCTCATGAGATCAGAACCCCAATGAATGGTGTTCTCG
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 3'ss of exon 6
gtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatag-------acatctcacttc-atacgttcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
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-tttattatttattattttattttattttattttctcacgtaaaaataaaacaaaataacacacaagcatgaaataacgacttgttgttgaacttgtgcagTTCTTGGCAACTGTGTCTCACGAGATTCGGACTCCAATGAATGGTGTTCTAGMapped 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|29630153|gb|CB635162.1|CB635162EST: TGAGCGAACTCAAGAAGCGTGCAGAAGATGCAGACGTCGCAAAGTCACAG TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTA
genomic: TGAGCGAACTCAAGAAGCGTGCAGAAGATGCAGACGTCGCAAAGTCACAGgtttttagtc ... ccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catccttctgagttaggatagacatctcacttcatacgttcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
atctcac putative branch site (score: 3)
cgttcttttccgctt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttagtcttacatctcacttccttctgcttgcacacatccttctgagttaggatagacatctcacttcatacgttcttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA