Sequence
atgc intronic sequence ATGC exonic sequence...cttactccttagaaatggtgatttgcagaaagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g51430.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 7
-----cttactccttagaaatggtgatttgcagaaagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
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gcagggcta-tccttagaactagtgatttgcagaatatttcctgatggttttcttat-ttttgccagcgtattaaattgtcacattcct---tgtttctgcacagGTATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAGAGATTCATTCAGATGCTTCGACTTCTCAGTGATAGAGCAAACGATATTCAAAATATAAAT
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 13
------------------------------------------------------------------------------------------cttactccttagaaatggtgatttgcaga-aagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
| || | ||| || || || || | ||||| || || || || | | | | | ||| || | || |||||| || || |||||||| |||||||| ||||| ||||| ||||| || |||||||||||| | || || || || || ||||| | |||| || |
gttttctctatattgaatatactacctttttaatcttcacagcttttggactggcttctctatgaaacacatcctaaacccatgcttgagcctatccgagtcaaactacacatttcacttaatctaaacaagtgtttattggtagagggcttctttatgtacatgttttatttgttctaattctg--gcagATACGAGATATTCCAGCTAATGGTAAATCTGTACACTGAGAGGTTTATTCAGATGCTAAGATTGCTTAGCGACAGGGCGAATGAATTAACAAACATTGAG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 12
--cttactccttagaaatggtgatttgcagaaagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
|| | | || | | | |||| | | | | ||||| | | || | | || | || | || || | |||||||||||| ||||| ||||||||||| || |||||||| |||||||| |||||||| || || |||||||| |||||||| | | |||||||| |
tgctcatttgttttgtacatttgtgtgcatctgtgtgttgtgaagact-ttcatccgtgaaaatgttttgtttgttcta-attcaatctttcttgattgcagATATGAAATATTCCAACTCATGGTAAATCTTTATACTGAGAGGTTCATTCAGATGCTTAGGCTGCTCAGTGACCGAGCAAATCAACTGACAAATATAGAG
upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 12
--cttactccttagaaatggtgatttgcagaaagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
|| | | || | | | |||| | | | || ||||| | | | || | | || ||| || | || || | | |||||||||||| ||||| || |||||||| || |||||||| |||||||| |||||||| || || |||||||| |||||||| | | |||||||| |
tgctcatttgtttcatgcatttgtgtgcatctgtgtgttgtgaagatt-ttcatccacgaaaatgttttgtttgt-tcaaattcaatctttcttgtttgcagATATGAAATATTCCAACTGATGGTAAATCTTTATACTGAGAGGTTCATTCAGATGCTCAGGCTGCTCAGTGACCGAGCAAATCAACTGACAAATATAGAGMapped 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|58665364|gb|CK054050.1|CK054050EST: GATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG ATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCA
genomic: GATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAGgtatgttgat ... ttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCA
EST:
gi|29666539|gb|CB662814.1|CB662814EST: GATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG ATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCA
genomic: GATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAGgtatgttgat ... ttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
cactaac putative branch site (score: 1)
tctcatgttttttttt putative PPT
atgtttttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttactccttagaaatggtgatttgcagaaagatacctagctgtttcttcatatcccactaacttctttcagtctcatgtttttttttgtttctatacagATATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAAAGGTTCATCCAGATGCTAAGACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - atttgca
- - - - - - - - - - - - - -gaaagata
- - - - - - - - - - - - - - - - - - ctagctg