Sequence
atgc intronic sequence ATGC exonic sequenceTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc...
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 14
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc----
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TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatattttatttcttgttgt-ggtcttggttttt-tcattagtgtttct--taacgcgccaagacaatgacagttgtcaatgtgataccttatctttaatat
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc---
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TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgttctcttgttgt-aatctttatattttttgttagtgtttct--taacgatccaagataatgacagctgtcggcgtgataccctattttgtacc
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 12
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc--
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TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTGgtaatatttgttttcttgttgttatcttgattttttttcattagtgtttct--taacgcgacaagacaacgacagctgtcaatgtgatactttatctttaat
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 12
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc--
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TGATCATGAAGGTGGAAATGTTAGTGCTCACGCTGGTCACCTGgtatgtatttgccacatgatcttgatgcatgataatgtt-ttgaacttatagacatt--tctgatggttctgtttttggctaatga-tgtttcttcacttag
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttt-tcaatgtt----gatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc
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TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttt----tgctaa-aaattcttgttca-tgtag--------
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 13
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaatta----ttgtttctttgttttca-----------atgttgatttttcttgt--tagtgttgctaa---cattgttttaacctgccaccggatcactgctggctgctgcatcatcc----------------------------------------------------------------------------
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TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTAgtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagaggaatgttctctattgactgatattatgctcaattcag
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 5'ss of exon 11
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc-
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TGATCATGAGGGTGGCAATGTAAGTGCTCATACTGTGCATCTGgtaagcagtgaattggatcctcctttcattctctgtcctctaaatgcgcaatatgctaaatcgaagttgctccgtcattttacttga-gctttacaatctaMapped 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|3758954|gb|C96653.1|C96653EST: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST:
gi|38470398|gb|CF954529.1|CF954529EST: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
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:
43 (upstream exon),
45 (downstream exon)
Score:
15TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc
- - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccaccg