Sequence
atgc intronic sequence ATGC exonic sequence...cttgtcatattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55360.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 5
-cttgtcatat-tatgtgcatgctattta-tctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
|| | || | ||| | | |||| | || | | | | || || | || | |||| | || | ||| ||| | ||| ||||||||| ||||||||||| || |||||||| ||||| ||| ||| ||| |||||||||||||||||||||||||||| | |||||||| |||||||||
ttgtggaagatatttgttccgattgtttaatttactcaagtaatttgtgttacgcaacgattaatgaacttggcgcatttacaatgttatgtt---tactcagGTTTCTTTTGCCTGCTTCACTTATTGTGATCAACGATATTTTTGCTTATTTATTTGGGTTCTTTCTTGGGAGAACACCATTAATCAAGTTGTCTCCAAAG
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 5
-cttgtcatat-tatgtgcatgctatttatctag---aaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
|| | || | ||| | | |||| || || | || ||| | | || || | ||||| | | || | || ||| | ||| ||||||||| ||||||||||| || |||||||| ||||| || ||| ||| |||||||||||||||||||||||||||| | |||||||| || ||||||
ctgtggaagatatttgtcctaattgtttaacttacgcaagtaatttgtattgt--gctacaattaatgaactctgtgcatttacaatggtatgtt---tactcagGTTTCTTTTGCCTGCTTCACTTATTGTGATCAACGATATATTTGCTTATTTATTTGGGTTCTTTCTTGGGAGAACACCATTAATCAAGTTGTCCCCAAAG
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
------cttgtcatattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
| | |||||| | || | | || | | || | | || | | || | | || | || | | ||||| |||||||||| | || || | || ||||| ||||| ||||||||||| ||| | ||||| ||||| |||| ||||| ||| |||| |||||||||||||||
gtttgaccattgctattatacgaataagacctgtcatgcactg--ttgcttcttaattgcattgatgttaatgtcttgc--ttgcattttgac-ctact-gtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
cttgtcatattatgtgcatgctatttatctagaaacagattacattatagac--accatttgacaaactccatataattcctttgtaatgctacttac---acagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
| || || ||||||| || | | || | | | || | | || | | | | ||| | || || |||||||||| | || || | || ||||| ||||| || |||||||| ||| | ||||| ||||| |||| ||||| ||| ||||||||||||||||||||
----taatgtttgaccattgctatt-atacgaataagacttgtcctgcacttttgcttcttaattgcattgatgttaatgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G02210.1 (Glycine max), 3'ss of exon 3
cttgtca--tattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
| || | | || ||| | | | || | || || |||| | | | | | | | | |||| || | |||||||| || ||||| ||||||| || || || ||| ||| ||| | || || |||| | ||||||||||||||||||||||| | |||||||||
-tgagcaactgctttggtattgccaaccactatgtttttcatgctttaattgattttattttttatagtt-acaacctaacatgttaatattatgatgaaagGTTTCTTTTCCCTGCAATCCTCATTGCTATGAATGATGTTGGTGCATATTTCTTCGGTTTCTATTTTGGGAGAACACCTCTGATCAAGCTTTCTCCAAAG
upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 5
cttgtcatattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattccttt------gtaatgc--tacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
| | ||| || || | | |||| ||| | | | |||| | || || | || ||| || | || | ||||||||| | || || || || ||||| || || || |||||||| ||| | ||||| ||||| |||| ||||||||| |||| ||||||||||||||
------aaggactttgccctttacttgattcttgagtgattggattgtcaagtc--tttggaattctttatttgtttattttcctgacatagtttagtatcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACACCTTTGATTAAGTTATCTCCAAAAMapped 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|29671303|gb|CB667578.1|CB667578EST: TTTGCACAATCTTCTTTTACCGTGGCAAATATATTTGAAGGGATGTTCTG GTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCT
genomic: TTTGCACAATCTTCTTTTACCGTGGCAAATATATTTGAAGGGATGTTCTGgtaagccata ... acttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCT
EST:
gi|29681974|gb|CB678249.1|CB678249EST: TTTGCACAATCTTCTTTTACCGTGGCAAATATATTTGAAGGGATGTTCTG GTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCT
genomic: TTTGCACAATCTTCTTTTACCGTGGCAAATATATTTGAAGGGATGTTCTGgtaagccata ... acttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
tacttac putative branch site (score: 1)
atataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtcatattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA