Sequence
atgc intronic sequence ATGC exonic sequencegtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70300.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G700866_T02 (Zea mays), 3'ss of exon 9
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
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gtatgtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgattttttcgcccctctttttcactac--------tagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTAGCAAGG
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300862_T05 (Zea mays), 3'ss of exon 8
gtctg-tagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTT-CTGGCAAAG------
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gtctggtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgatttttgcgcccctctttttcactac--------tagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTTCTGGCAAGGGTATGT
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300862_T02 (Zea mays), 3'ss of exon 9
gtctg-tagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTT-CTGGCAAAG
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gtctggtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgatttttgcgcccctctttttcactac--------tagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTTCTGGCAAGG
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G866647_T01 (Zea mays), 3'ss of exon 4
--------------gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
|| ||||| || | | || ||| || | |||||||| | | ||| ||| | ||| |||||| | | | || || | | ||| |||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | |||||||||||||| |
gggacatggataaggtttgtagtaggtaactttaaatatatcctcacatc-----cgcttgactttcgaggcattgattttttcgcccctctttttcactac--------tagATTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTGGCAAGG
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G169046_T01 (Zea mays), 3'ss of exon 1
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
|||||||| || | | || ||| || | |||||||| | || | | ||| |||||| | | | || || | | |||||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | |||||||||||||| |
gtctgtagtaggtaacttcaaatatatcctcacatccgcttgat---------gaggcattgattttttcgcccctctttttcactac--------tagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTGGCAAGG
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G166366_T01 (Zea mays), 3'ss of exon 3
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
|||||||| |||| | || ||| || | ||||| || | ||| | | | | |||||| |||| | | ||| || ||||||||||||||||||||||||||||||||||||||||| |||||||| || || |||||||||||||||||||| | || ||| || |||| |
gtctgtagtagataactttaaatatatcctcacgtc-----tgcttgacttttaaggctttgatttt-------ttgtccctcttttcactac---tagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACCATGTTGGACATCGTGAGCACTCGGATGCTTGGTCAGTATGTTTTCCTAGCAAGGMapped 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|29669913|gb|CB666188.1|CB666188EST: ACCCTAAAGCTCCAGGCACCCTGATCACTAAACAAAGAGAGATGGATAAG GTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
genomic: ACCCTAAAGCTCCAGGCACCCTGATCACTAAACAAAGAGAGATGGATAAGgtctgtagca ... ctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
ttttatttctattgtt CT-rich tract
attttatttctattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG