Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttcaatatctgataagatggcccacattagacttacagttgtctgtcttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g32850.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 2
ttgtttcaatatctgataagatggcccacatta--gacttacagttgt--ctgt----cttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG-------
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---------tatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactg-caaccgctgatgttaagttctt-at----gtacagcttgcagGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATGACCCAAC
upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G702490_T01 (Zea mays), 3'ss of exon 1
ttgtttcaatatctgataagatggcccacatta--gacttacagttgt--ctgt----cttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
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--atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactg-caaccgctgatgttaagttctt-at----gtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGGTATAATAACTGGCATAGGACCTGTTCATGGACGGTTATGTATGTTTGTGGCCAATG
upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G702490_T03 (Zea mays), 3'ss of exon 3
ttgtttcaatatctgataagatggcccacattagacttacagttgtctgtcttgttctagaatatcagctgttgatggtacctttt-ttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
| |||| ||| | | | ||| | ||| ||| | | | || | | | ||| | | ||| || | | | | | | | || || | || | | ||| | | || ||||| | || | | || || | | |||
---gtataataactggcataggacctgttcatggacggtta--tgtatgtttgtggccaatgacccaaccactaagggtggcacatactatcctcttactgtcaagaagcatctgcgagcacagGAAA----TAGCTTCGGAGTGCAAACTGCCTTGCATATATCTCGTTGACAG-CGGAGGTGCTAATCTCC--CCAG--
upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G702490_T03 (Zea mays), 3'ss of exon 2
ttgtttcaatatctgataagatggcccacatta--gacttacagttgt--ctgt----cttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
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--atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactg-caaccgctgatgttaagttctt-at----gtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG---------------------------------------------------------
upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0063g00290.t01 (Vitis vinifera), 3'ss of exon 2
-ttgtttcaatatctgataagatggcccacattagacttacagttgtctgtcttgttctagaatatcagctgt-tgatggtaccttttttatttcaa--taaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
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ttgaatgaaaaaattttctttatcaattg-attaaactt---gttatatgctttgagataatttattgtctatctgcttttagttgtattttttatggttaaagCTTGCAGGCCATGAGCTATATGAAGAACCTTTACCATCTGCTGGGATAATCACTGGAATAGGACCTGTGCATGGGCGACTTTGTATGTTTGTGGCTAATGMapped 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|29640036|gb|CB645045.1|CB645045EST: GCATCGACCGCCTGCTCGACCCCGGCGCCTCCTTCCTCGAGCTCTCCCAG CTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATACTA
genomic: GCATCGACCGCCTGCTCGACCCCGGCGCCTCCTTCCTCGAGCTCTCCCAGgtcggtctcg ... ttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtcttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
tgttgat putative branch site (score: 4)
taccttttttatttc putative PPT
taccttttttatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttcaatatctgataagatggcccacattagacttacagttgtctgtcttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA