Sequence
atgc intronic sequence ATGC exonic sequencegtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g10070.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
gtaatgctactagattga-tcaataattattgctcct-ttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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---acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaac-----accattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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------cttcttaagaatttttttccaat--ctcatccaatccatgtgtattgggaataaccgaacaaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
gtaatgc--tactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatg------------------ttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagt-ttacttccatctcattggcta-agaaataagaacatccttcacatttt-cagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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---------tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagt-ttacttccatctcattg--gctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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---------tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggct--aagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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------------------gtactacttat-actcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattgctgta-----tcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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----ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacag--tgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaatgctactagattgatcaa--taatta--ttgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatcctt---cacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattt-tgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAMapped 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|88825933|gb|CI776498.1|CI776498EST: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG GTCAAAAACCCAT
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCAT
EST:
gi|58608873|gb|CK036906.1|CK036906EST: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
EST:
gi|87021334|gb|CI295393.1|CI295393EST: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
EST:
gi|58694362|gb|CK083049.1|CK083049EST: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
EST:
gi|38481573|gb|CF965662.1|CF965662EST: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
42 (upstream exon),
63 (downstream exon)
Score:
28GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAGgtaatgctac ... acattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
tccttcacattttc CT-rich tract
taagaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC