Sequence
atgc intronic sequence ATGC exonic sequencegtaaattgatttacacaaccatacaattgccataagatgtgcatatatgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52690.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G445617_T01 (Zea mays), 3'ss of exon 10
gtaaattgatttacacaaccatacaattgccataagatgtgcata--tatgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
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gtacag-aatttacacagccatgtaattgt-gtgaaacgtgcatagtttttttttcagtt----ttccactgtcaatctcagGCTAGGTCTGCACGCCCATGTGTCATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCAGCAGATTCTGGCGGTGTCATGGACAGGG
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G058141_T02 (Zea mays), 3'ss of exon 1
gtaaattgatttacacaaccatacaattgccataagatgtgcatatatgcttacggttgcaactcttc--tgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
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gtacag-aatttacacagccatgtaattgt-gtgaaacgtgcata-attttttttttttcagttttccactgtcaatctcagGCTAGGTCTGCACGCCCATGTGTCATTTTCTTTGATGAGCTTGATTCCCTCGCTCCTGCACGAGGATCCTCAGCAGATTCTGGCGGTGTCATGGACAGGG
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 10
------------------------------------------------gtaaattgatttacacaaccatacaattgccataagatgt----gcatatatgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
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gtataataatattccggatttttttatctaaataatttctcaatttgagtaaatgtgtttgtgcctttttactgtgaactaaacagttttcagaacagattttgataaaatgaacttcaaaataattcacagGCCAGATCAGCACGTCCATGTGTCATCTTCTTTGATGAGCTTGATTCTCTTGCACCAGCTCGAGGTGCCTCTGGAGATTCTGGGGGTGTTATGGACAGAG
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaattg-atttacacaaccatacaattgccataagatgtgcatat-----atgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
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gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttct-tcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 10
gtaaattgatttacacaaccatacaat---------tgccataagatgtgcatatatgctt-acggttgcaactcttctgtcaacctc---agGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
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gtaaagatattcttatgtgattagaatgccttgttttgctctaacatgttttggttgacctcacaattctgtgacattgggcatcctttgtagGCAAGGTCAGCACGTCCATGTGTTATCTTCTTTGATGAACTTGATTCTCTTGCTCCAGCCCGAGGTGCCTCTGGGGATTCTGGGGGTGTTATGGACAGAGMapped 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|29675898|gb|CB672173.1|CB672173EST: ACATGTATGTTGGAGAATCGGAGAAGAATGTAAGGGACATTTTTGAGAAG GCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTT
genomic: ACATGTATGTTGGAGAATCGGAGAAGAATGTAAGGGACATTTTTGAGAAGgtaaattgat ... tcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTT
EST:
gi|58674677|gb|CK063364.1|CK063364EST: ACATGTATGTTGGAGAATCGGAGAAGAATGTAAGGGACATTTTTGAGAAG GCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTT
genomic: ACATGTATGTTGGAGAATCGGAGAAGAATGTAAGGGACATTTTTGAGAAGgtaaattgat ... tcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgccataagatgtgcatatatgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
tgcttac putative branch site (score: 2)
ctcttctgtc putative PPT
atatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattgatttacacaaccatacaattgccataagatgtgcatatatgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA