Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g57400.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G123544_T01 (Zea mays), 3'ss of exon 4
-------------gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactaga--gaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
| | | || | | | || | || || | ||| || | ||| | ||||| || | | || | || || ||||||||| |||||||||| || ||||||||||||||||| ||||||||||| | || ||||||||||||||||| || || ||||| ||||| |||||||
gtacgtatcagtcaagaaacgaaaatgagattgttcgtttagcctatgcttttttttttttttttttgcagatggcactgac-tatacgctacttctactgttgaccgacagATGGGATTAATGAAGAAGCATCCTTCCATAATACCATTCATGGTATACATCACAAACGAGGAGAAACACATGGAACGGTTTGCTGTGCGTGCGAAGTACA
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
||| || | | ||| | | | ||| ||||| | || | |||||| || | |||| | || ||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| | |||||||| ||||||||||| ||||| |||||||||||||||||||
gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt--agccactgat-taaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactg-------atgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
|| ||| | | ||| | | | | ||| || || | | | || ||| | | | | |||| | | || || || ||||||||||| ||||||||||| ||||| || |||||||||||| || ||||| | |||||||| |||||| |||| |||| ||||||||||||||||| |
gtatgtttgattttcattat-tgtgtccttca-ctatttcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
gtgcgttgcgtactagttag-atatttgcatcaattacttatactttg--ttgcatactagagaactgatg--tagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
|| ||| | | ||| | | | | ||| ||| | || || || || || | |||| | |||| || || ||||||||||| ||||||||||| ||||| || |||||||| ||| || ||||| | |||||||| || ||| |||| |||| ||||||||||| ||||| |
gtatgtttgattttcattattgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
upper sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 3'ss of exon 5
gtgcgttgcgt-actagttagatatttgcatcaattacttatactttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
|| || | | |||| || | ||| | | || | | | ||| | || | | | | || ||||||||||| ||||||||||| || || || |||||||| ||| ||||||| | ||||| || |||||| |||| ||||| ||||| ||||||||||| |
gtaagtgtcttcactaattctaattttttttttccttctcctgacaaggaatcttttagtgttttgtttttagttacaatggttgttccaattggcagATGGGGCTTATGAAGAAACATCCGTCAATCATACCATTCATGATATACATCACAAATGAAGACAAACACTTGGAACGATTTGCTGTTCGTGCAAAGTATAMapped 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|58691482|gb|CK080169.1|CK080169EST: GGGAG-TCATCTAAGCCTCAATTTTGTG ATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATT
genomic: GGGAGTTCATCTAAGCCTCAATTTTGTGgtgcgttgcg ... tttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATT
EST:
gi|33690965|gb|CF319204.1|CF319204EST: AGAAACAATCTGTAATTGTTGAGGGAGTTCATCTAAGCCTCAATTTTGTG ATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATT
genomic: AGAAACAATCTGTAATTGTTGAGGGAGTTCATCTAAGCCTCAATTTTGTGgtgcgttgcg ... tttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
aactgat putative branch site (score: 3)
ccttttctattttcat putative PPT
ttttctattttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactgatgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG