Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g58020.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
gtatg----ttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatc-tgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
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gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG-----
upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
----gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
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tactatataaacctttttgtgggggagaatgttgttaaa--ataatgac----atgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG-----
upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 11
gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatac----atcttttttttggtctcatgtttgatctgtta----tttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
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---------agtactaaataaacctgtgtgggggagaatgttat-taaaataatgacatgactctggtatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCAAATGGTATTGGCAAATCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGATCTGCTAAG-----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|58588466|gb|CF986774.1|CF986774EST: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST:
gi|218483226|gb|FG956166.1|FG956166EST: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
gtttgat putative branch site (score: 5)
ttatttc putative PPT
atacatctttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC