Sequence
atgc intronic sequence ATGC exonic sequencegttccatgctagcactgtttgtttttttgttctgtgatttgtgctaagaggtttttacttgaagtgcttactacccttttgttttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01890.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 5
gttccatgctagcactgtttgtttttttgttctgtgatttgtgctaagaggtttttacttgaag-tgcttactacccttttgttttcatgatgt-aagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
||| ||| | | | | | |||||| || || | || ||||| | || |||| | | | || | | | ||||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||
gttatatgtcaac----tctcaatccctgttctttggcttaagttacattttttttccagaaaactgctaggtgctaactacattctgttttctgaagCCTGGTCCGGATTCAGTTGGTATCGTGGCCATTTCGCATGGTTGCCGTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA
upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 5
gttccatgctagcact-gtttgtttttttgttctgtgatttgtgcta---agaggtttttacttgaagtgcttactacccttttgttttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
||| | | | | || || || || | | | | | || | | || | | || | |||| ||||| |||||||||| |||| ||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||
gttataagtcaactctcaattcttgttctttcccttaagttacattttttacagataagtgct--acttgctaactaca-ttttgttttc-tgat--tagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCGCATGGTTGCCGTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA
upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------gttccatgctagcactgtttgtttttttgttc--tgtgatttg-tgctaagaggtttttacttgaagtgcttactacccttttgt-----------tttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
| ||| | || || | ||| |||||| | |||| | | |||||| | ||| | || || | || || || |||||||||||||||||||||| || | ||||||||||| ||||| |||| || || || || ||||||||| | || | ||||||| || ||
gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatacggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------gttccatgctagcactgtttgtttttttgttctgtgat-ttgtgctaagaggtttttacttgaagtgcttactacccttttgttt----------tcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
| | | || ||||| ||| |||||| | | || ||| || | || | || | || | | || | || |||||||||||||||||||||| || | ||||||||||| ||||| |||| || || || || ||||||||| | || | ||||||| |||||
gttttttttttcttttctgttccttgcaatgaatttgttaagaaattggtgacctttggcatctagaggacagcttttgtgaattt-cgttgtgataccccgttttgaattttcta---aatttgtcaattatctcttcatctaagaaaaagttctttttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACAAAG
upper sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------gttccatgctagcactgtttgtttttttgttctgtgatttgtgctaagaggtt----tttacttgaagtgcttactacccttttgttttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
| ||| ||| ||| || | | | ||| | || | | | | ||| || || | ||| | || ||| ||| |||||||||||||||||||||| || | |||||||||||| ||||| |||| || || || || || || ||| | || | ||||||| ||||
gttttgcattttcttctataaagaattgttttcttcttcattctatatgcttttattgatatagtgtgtttctcacaatataatgctgaagcgtttctgagttgattgtttaattttgttgttgatgctgtcagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACATAGTTGCAGTGGAGTGGCAGCTCGAGCATGCGGTCTTGTAAGTTTAGAACCCTCAAAGMapped 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|29634707|gb|CB639716.1|CB639716EST: CAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG CCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGT
genomic: CAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAGgttccatgct ... atgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGT
EST:
gi|29642722|gb|CB647729.1|CB647729EST: CAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG CCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGT
genomic: CAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAGgttccatgct ... atgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctaagaggtttttacttgaagtgcttactacccttttgttttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
tgcttac putative branch site (score: 2)
cccttttgttttcat putative PPT
tttttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttccatgctagcactgtttgtttttttgttctgtgatttgtgctaagaggtttttacttgaagtgcttactacccttttgttttcatgatgtaagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCACATGGTTGCCGTGGTGTTGCTGCCCGTGCCTGTGGTTTGGTGAACCTAGAACCAACAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC