Sequence
atgc intronic sequence ATGC exonic sequencegtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctttctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g48370.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G110109_T01 (Zea mays), 3'ss of exon 11
gtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactcttt----ctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
||| |||| || |||||| ||||| | ||| |||| ||| ||||||| ||||||| | | | ||||||||||||| |||||| || ||||||||||| ||||||||||| ||||||||||||||||| || ||||| || |||||||||||||| ||| ||||||
gtggtagcttcactttgaacactaacagaaacacatttgtgaactcagtt--taacatgtagtgatttttttgtttgcctcagGTGGTCAACTTGCCATCAAGAATCGATCCTCACCAAACATCCGCTGTTGTCACGCTTCATGGTCAGCTATTCGTGCGTGCACCATTTGGTCATCCTGATA
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G180223_T01 (Zea mays), 3'ss of exon 4
--gtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctttctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGG-CATGCTGATA
| || || || | || | | ||| |||| || ||||||| ||||||| | | |||||||||||||| |||||| || ||| ||||||| ||||||||||| |||||||||||||||| || | ||||| ||||||||||||||| ||| |||||
gtggtatgctgacagcttcactatcag---aaacacatttgtgaattcagtt--taacatgtagtgatt-ttttatctcagGTGGTCAACTTGCCATCAAGAATCAATCCTCACCAAACATCCGCTGTTGTCACGCTTCATGATCAGTTGTTTGTGCGTGCACCATTTGGGTCATCCTGAT-
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G421899_T01 (Zea mays), 3'ss of exon 11
gtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctt-tctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
|| | ||| || | || | | ||| |||| || ||||||| ||||||| | || |||||||||||||| |||||| || ||| ||||||| ||||||||||| ||||||||||||||||
gt-aggctgacaacttcactatcag---aaacacatttgtgaattcagtt--taacatgtagtgattttttttatctcagGTGGTCAACTTGCCATCAAGAATCAATCCTCACCAAACATCCGCTGTTGTCACGCTTCATG---------------------------------------
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G421899_T03 (Zea mays), 3'ss of exon 10
gtgatag--cagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctt-tctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGG-CATGCTGATA
||| ||| ||| || | || | | ||| |||| || ||||||| ||||||| | || |||||||||||||| |||||| || ||| ||||||| ||||||||||| ||||||||||||||||| || || ||||| ||||||||||||||| ||| |||||
gtggtaggctgacaacttcactatcag---aaacacatttgtgaattcagtt--taacatgtagtgattttttttatctcagGTGGTCAACTTGCCATCAAGAATCAATCCTCACCAAACATCCGCTGTTGTCACGCTTCATGGTCAGCTGTTTGTGCGTGCACCATTTGGGTCATCCTGAT-
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G161854_T01 (Zea mays), 3'ss of exon 2
gtgatag--cagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactcttt--ctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGG-CATGCTGATA
||| ||| || || | || | | ||| |||| || ||||||| ||||||| | ||| ||||||||||||| |||||| | ||| ||||||| ||||||||||| ||||||||||||||||| || || ||||| ||||||||||||||| ||| |||||
gtggtaggttgacagcttcactatcag---aaacacatttgtgaattcagtt--taacatgtagtgatttttttttatctcagGTGGTCAACTTGCCATCAGGAATCAATCCTCACCAAACATCCGCTGTTGTCACGCTTCATGGTCAGCTGTTTGTGCGTGCACCATTTGGGTCATCCTGAT-
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G421899_T02 (Zea mays), 3'ss of exon 10
gtgatag--cagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctt-tctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
||| ||| ||| || | || | | ||| |||| || ||||||| ||||||| | || |||||||||||||| |||||| || ||| ||||||| ||||||||||| ||||||||||||||||
gtggtaggctgacaacttcactatcag---aaacacatttgtgaattcagtt--taacatgtagtgattttttttatctcagGTGGTCAACTTGCCATCAAGAATCAATCCTCACCAAACATCCGCTGTTGTCACGCTTCATG---------------------------------------
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ17697 (Selaginella moellendorffii), 3'ss of exon 10
gtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctttctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCA-TGCTGATA
|||| | | || | | | |||||| | | | | | || | || |||||| |||||||||| | | ||||||| ||||||||||||| |||||||| ||||| || || || || || | | | ||||| | || | | |
------------gtttgggtttt--cttctttcagctaccgttctctccgggaagttttttctcatcgat-ttgtgcagGTGATCAATCTGCCGCTAAAGATCGATGCTCATCAAACATCGGCCGTTGTTACGCTCCACGGGCAGCTGTTCATCAGAGTTCCATTCGCTCAATCTTCGT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgagcacgtttgcattctcttcagataacatgaagtgattactctttctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
ttactctttctc CT-rich tract
ataacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatagcagcaatttgaatactaatttgagcacgtttgcattctcttcagataacatgaagtgattactctttctcagGTGGTCAATCTGCCATTGAGGATCGATCCTCATCAAACATCCGCCGTTGTCACGCTTCATGGCCAACTATTTGTTCGTGCACCATTTGGGCATGCTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT