Sequence
atgc intronic sequence ATGC exonic sequenceTCTTTCAAGGTTCAGCAGTTGTATTATGCTTGTGGCATATGCAAGCTATCTCTATTTCCAACTAAGTGGACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgtatacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55940.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143356_T01 (Zea mays), 5'ss of exon 7
--TCTTTCAAGGTTCAGCAGTTGTATTATGCTTGTGGCATATGCAAGCTATCTCTATTTCCAACTAAGTGGACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgt-atacctcaatttaattcttcattgatggtgacaaatatgatatgcttg-cactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatag
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GCTCTTTCAAGATTCAGTAGCTGTATTATGCTTGTGGCGTATGCAAGCTACCTCTATTTCCAATTAAGTGGACGGAGCAACATTTACAGTCCAATAGGCAgtgtaagtttgatgtctcatcttattttttcctcactggtaataagaaccataaccatgacactatgatttctatcgt--aggtatgg-ctattttagtctac--------------------------------------------------------------
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G040017_T02 (Zea mays), 5'ss of exon 6
TCTTTCAAGGTTCAGCAGTTGTATTATGCTTGTGGCATATGCAAGCTATCTCTATTTCCAACTAAGTGGACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgt-atacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaa---tgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatag
|||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||| |||||||||||| || ||| |||||||| |||||||||||| | || ||||| ||| |||||| | | |||||| || | ||| || | |||| | || | | || ||| |||
ACTTTCAAGGTTCAGTAGTTGTATTATGCTTGTGGCGTATGCCAGCTATCTCTATTTCCAATTAAGTGGACGGAGCAACATTTACAGTCCAATAGGCAGTgtaagtttgatgcctcatcttatttcttcctcgctggtgataaggaccataactgtgatgctataatttctattgtcagtatggctagtttagtctactt-----------------------------------------------------------------
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143356_T02 (Zea mays), 5'ss of exon 7
TCTTTCAAGGTTCAGCAGTTGTATTATGCTTGTGGCATATGCAAGCTATCTCTATTTCCAACTAAGTGGACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgt-atacctcaatttaattcttcattgatggtgacaaatatgatatgcttg-cactttgaattggaac--aacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatag
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TCTTTCAAGATTCAGTAGCTGTATTATGCTTGTGGCGTATGCAAGCTACCTCTATTTCCAATTAAGTGGACGGAGCAACATTTACAGTCCAATAGGCAGTgtaagtttgatgtctcatcttattttttcctcactggtaataagaaccataaccatgacactatgatttctatcgtaggtatggctattttagtctactt-----------------------------------------------------------------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|286840|gb|D15647.1|D15647EST: GACGGAATAATGCTTATAGTCCAATTGGCAGT GAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATT
genomic: GACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgtat ... cctgtcatagGAAGAAATGCCCAATGAGGATGCAGCAGAGGAAGATGAAGAATCAGAGATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTTCAAGGTTCAGCAGTTGTATTATGCTTGTGGCATATGCAAGCTATCTCTATTTCCAACTAAGTGGACGGAATAATGCTTATAGTCCAATTGGCAGTgtaagtgtatacctcaatttaattcttcattgatggtgacaaatatgatatgcttgcactttgaattggaacaacaagcaatgaactaatctccttgataacagtcagttacattccctaaaaataaaaatgtaatatccatgttccatcgcctgtcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA