Sequence
atgc intronic sequence ATGC exonic sequenceGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063909_T02 (Zea mays), 5'ss of exon 2
GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
|| ||||||||||||||||| ||||||||||||||||||||||||||||| | || || || ||| |||| | || | || | || | | || | || | | |||||| || || ||| | | | | |||| | || | | | |||| ||
GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTCgtaggacagc--tcgtcttcctgctgctctacattgccgtaaacac-gtagagctgtgcatg--tgctatggatggga----tgctgatactgtgtgttt--ctgcaaattaaatgcag----------------------------------------------------------
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 3
GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
|| ||||||||||||||||| || |||||||| ||||||||||||||||| | || ||||| |||||||| | | || | |||| | || | | || | | | | || || | | |||| || ||| | | | |
GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt--tcgtcttcctgttatgccttgtggtaga--gttttgtgtac-tctggatagc--atgctgattgt--gtttctgcaaatgcag----------------------------------------------------------------------------------
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 3
GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
|| ||||||||||||||||| ||||||||||||||||||||||||||||| | || ||||| |||||||| | | | || | | | | | |||| | | | | | | || |||| || |||| || | | | | | |
GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt-----tcggcttcctgttgtacct-tgtgttagagttgtgtac-tctggatgg--gatgctgattgt--gtttttgcaaatgcag----------------------------------------------------------------------------------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|88695722|gb|CI737760.1|CI737760EST: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcag
- - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - CAGATG