Sequence
atgc intronic sequence ATGC exonic sequencegtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70300.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G700866_T02 (Zea mays), 3'ss of exon 9
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
|| ||||| || | | || ||| || | |||||||| | ||| ||| | ||| |||||| | | | || || | | | ||||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | ||||||||| |||| |
gtatgtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgattttttcgcccctctttttcactact--------agGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTAGCAAGG-------
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300862_T05 (Zea mays), 3'ss of exon 8
gtctg-tagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTT-CTGGCAAAGGTATGTT
||||| ||| || | | || ||| || | |||||||| | ||| ||| | ||| ||||| ||| | |||| |||||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | ||||||| ||||||| |||||||
gtctggtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgattt--------ttgcgcccctctttttcactactagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTTCTGGCAAGGGTATGT-
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300862_T02 (Zea mays), 3'ss of exon 9
gtctg-tagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTT-CTGGCAAAGGTATGTT
||||| ||| || | | || ||| || | |||||||| | ||| ||| | ||| ||||| ||| | |||| |||||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | ||||||| ||||||| |
gtctggtagtaggtaacttcaaatatatcctcacatc-----tgcttgactttcgaggcattgattt--------ttgcgcccctctttttcactactagGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTTCTGGCAAGG-------
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G866647_T01 (Zea mays), 3'ss of exon 4
--------------gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
|| ||||| || | | || ||| || | |||||||| | | ||| ||| | ||| |||||| | | | || || | | | || |||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | |||||||||||||| |
gggacatggataaggtttgtagtaggtaactttaaatatatcctcacatc-----cgcttgactttcgaggcattgattttttcgcccctctttttcactact--------agATTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTGGCAAGG-------
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G169046_T01 (Zea mays), 3'ss of exon 1
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
|||||||| || | | || ||| || | |||||||| | || | | ||| |||||| | | | || || | | | ||||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| | |||||||||||||| |
gtctgtagtaggtaacttcaaatatatcctcacatccgcttgat---------gaggcattgattttttcgcccctctttttcactact--------agGTTGTACTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGACATTGTGAGCACTCGGATGCTTGGTCAGTATGGTTTTCTGGCAAGG-------
upper sequence: LOC_Os01g70300.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G166366_T01 (Zea mays), 3'ss of exon 3
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
|||||||| |||| | || ||| || | ||||| || | ||| | | | | |||||| |||| | | ||| || ||||||||||||||||||||||||||||||||||||||||| |||||||| || || |||||||||||||||||||| | || ||| || |||| |
gtctgtagtagataactttaaatatatcctcacgtc-----tgcttgacttttaaggctttgatttt-------ttgtccctcttttcactac---tagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACCATGTTGGACATCGTGAGCACTCGGATGCTTGGTCAGTATGTTTTCCTAGCAAGG-------Mapped 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|58597397|gb|CK007925.1|CK007925EST: CCCTAAAGCTCCAGGCACCCTGGATCACTAAACAAAGAGAGATGGATAAG GTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
genomic: CCCTAAAGCTCCAGGCACCCT-GATCACTAAACAAAGAGAGATGGATAAGgtctgtagca ... ctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
EST:
gi|29669913|gb|CB666188.1|CB666188EST: ACCCTAAAGCTCCAGGCACCCTGATCACTAAACAAAGAGAGATGGATAAG GTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
genomic: ACCCTAAAGCTCCAGGCACCCTGATCACTAAACAAAGAGAGATGGATAAGgtctgtagca ... ctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtagcagattaattaaaacatgttctcacatcagtaccattcaactctcgggccatggattttatttctattgttctttatttttctctggatagGTTGTGCTAACTAGCATAGTGCTCAAGTCAAATGTCACTATGTTGGATATAGTAAGCACTCGGATGCTTGGTCAATTTGGTTTTCTGGCAAAGGTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG