Sequence
atgc intronic sequence ATGC exonic sequence...ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g35050.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G163334_T01 (Zea mays), 3'ss of exon 4
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttct-tatcattcatttcatggactggt---atagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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----ggagaactgcgcatcttatatattagagaggaataaaaaccttacaaaaaggagatgttgctgagctatgtttgatttattgcatgcacttgttttgtagGTGGTTTACAATGCAAATAAACTTGCTAAATTGGTGAAAGAGAAAGCAAAGATGCATAATTGGCTTGACTACTATCAGCTGAGATTTGAAAGGAATGCAT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 5
--ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatttcatggactggt---atagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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atttttgtttgattccttgtaatttatttttaaaattgtttttctgtaaaacagaatcagaca-tgctatgtt----tgatttattgcatgcacttattttgtagGTGGTTTACAATGCAAATAAACTTGCTAAATTGGTGAAAGAGAAAGCAAAGATGCATAATTGGCTTGACTACTATCAGCTGAGATTTGAAAGGAATGCAT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 5
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccac-taccat-gttcttatcattcatttcatgg--actggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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--cccttcaatcacatatcataaattctagtaggctgtttat--tgtgttttatcctaccacgtacttttgtttttttccttacttttaaaggtatttctgcagGTTGTTTACAATGCAAAGAAACTTTCTAGTCTTGTTTCAAAGAAGAAGAAAAGGCAGAATTGGCTTGACTACTATGAACTTAAATATTCTAGAAATCAAT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 5
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggctt-------accactaccatgttcttatcattcatttcatgg-actggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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-------gatctatctattattacgacaatgtaattttcccctttcatttgggactttgagaggggggaaataatgtt-tcagcatatttattgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 4
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatt-tcatgg-actggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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-ttattgcgacaatgtcatttttccctttcatttgggactttgagggggggggggggggga-taatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
-ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgat-atggcttaccactaccatgttcttatcattcatttcatggactggtat--agGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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gcaagttccttagaagttttaaatttgaaaccgtttagttttctttaaaattatgctcttcttgagatgtaagaacaacataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 5
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcat-tcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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--------------------gtactacaactttggt-tgtctaacttaggatgttccatgttttcggtgtattcatcttctcgtttaacaaa-----acagGCGGTCTACAACGCAAACAAGCTGTCGGAACTGGTACAGAAGAGGATGAAATTGCAGAATTGGCTTGATTACTATCAAAACAAACACTCTAGGAATCCAT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G62320.1 (Arabidopsis thaliana), 3'ss of exon 4
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
||| | | | ||| ||| || | || || ||| ||| | ||| || | || | | |||| || || ||||||||| | | | ||| |||| |||| ||||||||||||||||||||| | |||||||| ||| |||| ||| |||||| |
-------------gttag-atcatagcattaaaggaatgaatatttcttta-ggtttattgctattcgttaagtatt-ttagacttatatat--atccagGTGGTGTACAATGCAAATGAATTGGCTAAATTGGTAGAAGACAAGAAGAAAATGCAGAATTGGTTAGATTACTACCAGTTGAAGTATACAAGAAACAAGG
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 4
ttagttttaactgcttatcgttacta--aaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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tttctttagaaaatctagtataaacattgaaatgggtaattcaaaatataaagca--ttaaaatgtttatattcaatttcctaatttagaagttttatgcagGTTGTATATGATGCAAATAAACTTGCAAAATTGGTCAAGAAGAAGGAAAAAATGCAGAATTGGCTTGACTATTATCAAATTAAATATTCTAGAAATGAATMapped 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|58609230|gb|CK037263.1|CK037263EST: TGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACCAG GTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAA
genomic: TGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACCAGgtaatattta ... actggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatatggcttaccactaccatgttcttatcattcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
ggcttac putative branch site (score: 3)
ttatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatttcatggactggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA