Sequence
atgc intronic sequence ATGC exonic sequence...gcatattgtttgtacctgatggttcatggcatgatgcattcatgcatattgtttgtacctgatggcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g07880.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G005848_T01 (Zea mays), 3'ss of exon 13
gcatattgtttgtacctgatggttcatggcatgatgcattcatgcatattgtttgtacctgatg--gcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
||| | | | || ||| || | || ||| || ||| || |||| | || | || || | | | ||||||| |||||||| ||||||| ||| |||||||||||||||||||||||||||||||| |||
tcatcactgctaaatcacatccttcttgtttccactgatatgcttctatagtctgtgttaattgttacatggataatatagattttta--tttcaaatgcagGTGTATGGAAGATTTGGAGAGTACCACTCGTTATGTCACTTGGTCCCTTCACAACAAG
upper sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 9
-gcatattgtttgtacctgatggttcatggcatgatgcattcatgcatattgtttgtacctgatggcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
||| || | | | | |||| | | || |||| || | || | ||| | ||| | | | | ||||||||||||||| |||||||||||||| || ||||| | ||| | || |||||||||
gatttatcccttttcttttttcatacatgatacctattaaatattagtattccaggttgtttatttgcttttttctaaattccttgct-tctctgctacagATGTATGGAGGACTTGGTGAGCACCACACGGTATGTTTCATGGCCTCTCCACAATAAG
upper sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 13
gcatattgtttgtacctg-atg-gttcatggcatgatg--cattcatgcatattgtttgtacctgatggcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
| || || | | || || | || || || ||| | | | || | | | |||| ||| || | | ||| | | |||||||| ||||| || || ||||||||||| ||||||||||||||||| || |||||||||
-aagcttcttcattcttgtgtgcatctattgcttgccaactattatttttaactcattaagctttgta--ctgatgtatactcacttagtaatat-cattgcagATGCATGGAAGACTTAGTGAGCACCACCCGTTATGTCACTTGGTCTCTCCACAATAAG
upper sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S304_66V6.2 (Physcomitrella patens), 3'ss of exon 15
------gcatattgtttgtacctgatggttcatggcatgatgcattcatgcatattgtttgtacctgatggcatgatttatctgc-atgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
||| | ||| ||||| | | || ||| ||| || || ||| || | | | ||| | || || || |||| ||||||||||||||||| | |||||||||| || |||||||||||||| ||||| ||||||
agtcatgcagacgacttg--gttgatgactgtatctaatatattttcctgc-taatgaatgtctctcctttctttgttttttcatgattttcaattgtg----gcagATGTATGGAGGATCTAATGAGCACCACGCGGTATGTCACTTGGTCACTTCATAATAAGMapped 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|88570954|gb|CI662327.1|CI662327EST: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAG ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
genomic: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAGgtaatactgt ... tgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
EST:
gi|88349832|gb|CI634367.1|CI634367EST: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAG ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
genomic: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAGgtaatactgt ... tgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
EST:
gi|88326033|gb|CI651082.1|CI651082EST: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAG ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
genomic: GCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAGgtaatactgt ... tgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
67 (upstream exon),
30 (downstream exon)
Score:
7AAGATGGTGAGAACTGTAGCAGCCATGATGTACTTGTGAAGCGTGTCAAAGCTGCATTTGATAGGTTTGCTGAATCTACTGAGCAATCATGTCGTGAAAGgtaatactgt ... tgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgtttgtacctgatggcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
acctgat putative branch site (score: 7)
atgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatattgtttgtacctgatggttcatggcatgatgcattcatgcatattgtttgtacctgatggcatgatttatctgcatgttgaaatgtgtaatgcagATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG
- - - tgtttgt
- - - - - - - cctgatg
- - - - - - - - - - -gttcatg
- - - - - - - - - - - - - - - -tgatgca
- - - - - - - - - - - - - - - - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttg