Sequence
atgc intronic sequence ATGC exonic sequence...tctttgagttttaattgttgagaaaatgcatatacatgcaggatatgtatgaattttaatgaatactggcatgagaacctcacatactgtacttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 16
------tctttgagtttta--attgttgagaaaatgcatatacatgcagGATATGTATGAATTTTAATGAATACTGGCATGAGAACCTCACATACTGTACTTATGCAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
|||| || | ||| || ||||| ||| || | || | ||| |||| ||| | |||||||||||||| | || |||||||||||||||||||||| ||||| || || ||||| |||| |||| |||||||||||| |||||||| ||||| ||||||||||||||||||||||| ||||
atttggcctttttcttccactattctttgaaaaatacatgtagaaacacg--------gaacaataataaatggtaacatgagaacctcactggttctatttatgcagGATATGTATGATTTCATGGCCCTCGATAGACCTTCAACTCCTACCATTGATCGTGGGATAGCATTACATAAGATGATTAGACTTATCACAATGGGTTTAG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 16
tctttgagttttaattgttgagaaaatgcatatacatgcagGATATGTATGA-ATTTTAATGAATACTGGCATGAGAACCTCAC----ATACTGT--ACTTATGCAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
| | || | | | | | | | ||| ||| || | | | | | | | | | | || | |||| || | |||||||||||||| || |||||| | |||||||| | ||||||| || |||||||| ||||| ||||| ||||||||||| ||||| || ||||| | |
-------ctgtcaaatcatttaaggacacttgtgtttgctttataagtgtattgctgcagtttgtcatttgacaaatattttactaatgttctgttggctgcttcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACACCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 16
tctttgagttttaattgttgagaaaatgcatatacatgcagGATA--TGTATGAATTTTAATGAATACT-GGCATGAGAACCTCACATACTGTACT---TATG-CAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
| | || | | || | | ||| ||| ||| ||||| | | | | | ||| | || | | | | | |||||||||||||| || |||||| | |||||||| | || |||| || |||||||| ||||| ||||| ||||||||||| ||||| || ||||| | |
-------ctgtcaaattatatgaggacacttatgtttgctttataagtgtattgctgcagtttgccatttgacatatattttactaatgttctgttggctgcgtcagGATATGTATGACTTCATGGCTTTAGACAGACCATCCACTCCTATTATAGATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGCCTTG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 16
tctttgagttttaattgttgagaaaatgcatatacatgcagGATATGTATGAATTTTAATGAATACTGGCATGAGAACCTCACATACTGTACTTATGCAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
| | || || || | | | | | || || | | | | | ||| || | | | ||||||||||||||||| ||||| | |||||||| |||| ||| || ||| | |||||||| ||||| ||||||||||| ||||| || ||||| ||||
-------------------gtatagatagat-tagacaccgt-tttacattaaactcattattaaaagttatgtgagcggtgttgttcgggttc---cagGATATGTATGATTTCATGGCAGTAGACAGACCATCAACTCCTCTTATCGATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 16
tctttgagttttaattgttgagaaaatgcatatacatgcagGA-TATGTATGA-ATTTTAATGAATACTGGCATGAGAACCTCACAT-ACTGTACTTATG---CAGGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
|| || ||| | | || ||| | || | | ||||| | || || || ||| || || | || | | | |||| |||||||||||||| || |||||| |||| || || |||| ||| || ||||||||||||||||| || |||||||| |||||||| || ||||| ||||
-----tggtcaagatagtt-acagtgtgtttatgctaccaaaagtgcatatgacaggcctatatattttgacattttaatcttatattatggaatttatttttcagGATATGTATGAATTCATGGCTTTGGATAGGCCAACAACTCCTGCTATAGATCGTGGAATAGCATTACACAAAATGATCAGACTTATTACCATGGGCTTAGMapped 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|2796466|gb|AA749760.1|AA749760EST: ATCAAGCACTAGTTGGTGACAAAACTATTGCATTCTGGTTGATGGACAAG GATATGTATGATTTTATGGCTCTGGACAGACC
genomic: ATCAAGCACTAGTTGGTGACAAAACTATTGCATTCTGGTTGATGGACAAGgttaccacac ... acttatgcagGATATGTATGATTTTATGGCTCTGGACAGACC
EST:
gi|2798079|gb|AA751373.1|AA751373EST: GACAAAACTATTGCATTCTGGTTGATGGACAAG GATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
genomic: GACAAAACTATTGCATTCTGGTTGATGGACAAGgttaccacac ... acttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
EST:
gi|2798126|gb|AA751420.1|AA751420EST: ATCAAGCACTAGTTGGTGACAAAACTATTGCATTCTGGTTGATGGACAAG GATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
genomic: ATCAAGCACTAGTTGGTGACAAAACTATTGCATTCTGGTTGATGGACAAGgttaccacac ... acttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
EST:
gi|66947037|gb|AU311881.1|AU311881EST: CAAAACTATTGCATTCTGGTTGATGGACAAG GATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
genomic: CAAAACTATTGCATTCTGGTTGATGGACAAGgttaccacac ... acttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGAT
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:
75 (upstream exon),
60 (downstream exon)
Score:
630GACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAAGCACTAGTTGGTGACAAAACTATTGCATTCTGGTTGATGGACAAGgttaccacac ... acttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatgaattttaatgaatactggcatgagaacctcacatactgtacttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
acctcac putative branch site (score: 630)
aattttaatgaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgagttttaattgttgagaaaatgcatatacatgcaggatatgtatgaattttaatgaatactggcatgagaacctcacatactgtacttatgcagGATATGTATGATTTTATGGCTCTGGACAGACCGGCAACACCTAGCATTGATCGTGGAATAGCATTGCATAAAATGATTAGACTTATCACAATGGGGTTAG
- - - - - - - ttgttga
- - - - - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - tacatgc
- - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatac