Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCCCCCAAGCCTGCAGCCAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47180.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47180.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G43980.1 (Glycine max), 3'ss of exon 4
gtgagtttcttcttgattagtagttttgcagtcac-tgcctataa-gttaatct----gttatttgctgatcgtcttactgt--gattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCC---CCCAAGCCTGCAGCCAAGG
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gtaatttatttttggatt--ttgttgagcagaaacctgattagattgtctattttgaggcttttttctgattagtgcaatgccaaacttcctttcagAGTCCGGATGGTTGCACAGTAGCATCAGCAGCGGCAGATGAAACACTGAGGTTTTGGAATGTGTTTGGAGCTCCGGAAGCAGCATCTAAGGCTGCACCGA---
upper sequence: LOC_Os02g47180.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G01450.1 (Glycine max), 3'ss of exon 3
gtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCC---CCCAAGCCTGCAGCCAAGG
|| | ||| |||| || | | | | || | | | || | ||| ||||| | ||| | || |||||||| |||||||||||||||||||| || || |||||||| || || ||||||||||||||||||| ||| ||||| | ||| ||||| | |
gt-aattttttctcgagcacaaacctgattgat-ttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcagAGTCCAGATGGTTGCACAGTAGCATCAGCAGCAGCAGATGAAACATTGAGGTTCTGGAATGTGTTTGGAGCTCCAGAAGCAGCATCTAAGGCTGCACCGA---
upper sequence: LOC_Os02g47180.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------gtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCCCCCAAGCCTGCAGCCAAGG
| | ||| | || | | ||| || | | | || | ||| || | | | ||| || |||||||||| |||||||| || ||||| || || || | ||||||||| ||| ||||||||||||| ||||| || || || |||| || ||
gtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttg-tgttgtttgtgttgtattt--cttacagAGTCCAGATGGTTGTACCGTAGCTTCAGCAGCAGGAGATGAGACTCTGAGGTTCTGGAATGTTTTTGGAGTACCAGAGACCGCCAAAAAAGCTGCTCCAAMapped 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|325493626|gb|JG458150.1|JG458150EST: AGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAG AGTCCTGATGGTTGCACAAGTAGCATCGGCTGCTGCAGATGAGACCCTGCG
genomic: AGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttct ... tgaactacagAGTCCTGATGGTTGCACA-GTAGCATCGGCTGCTGCAGATGAGACCCTGCG
EST:
gi|66915812|gb|CX102660.1|CX102660EST: GATGGCTGAACTCACTGGCCATAACT-CCCGTGTCCTTTTCATGGCTCAG AGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGAACCTGCGG
genomic: GATGGCTGAACTCACTGGCCATA-CTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttct ... tgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCCCCCAAGCCTGCAGCCAAGG
gtcttac putative branch site (score: 3)
ttaatctgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacagAGTCCTGATGGTTGCACAGTAGCATCGGCTGCTGCAGATGAGACCCTGCGGTTCTGGAATGTGTTTGGTAGTCCTGAAGCCCCCAAGCCTGCAGCCAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG