Sequence
atgc intronic sequence ATGC exonic sequenceGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctaccctctttctgatactgatcaaactggagttatggctgatctgttaggggccatcctaggtgttgcaacttcaaataaattgttctctggt...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16290.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G111014_T01 (Zea mays), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctaccctctttctgatactgatcaaactggagttatggctgatctgttaggggccatcctaggtgttgca-acttcaaataaattgttctctggt-----
||| ||||| || |||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| ||||||||||||||||| |||||||| |||| | ||| || | | | || |||| || || ||||||||| | | || || | | ||| |||
GGAGGCTCTCCGGTATCATAAGATAGTTATACTTACTGACGCTGATGTTGATGGAGCACATATCCGGACTCTCCTCCTTACTTTCTTCTTCAGATATCAAgtacgt--accaagaatcatctgcacactgaa---gagt-atacctcatctgttagattcttcatttataagtgtgtaccaagagggacctgtaaactgaagagta
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA03G28290.1 (Glycine max), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtact-tctaccctctttctgatactga----tcaaa--ctggagtta--tggctgatctgttaggggcca--tcctaggtgttgcaacttcaaataaattgttc--tctggt--------------------
||| || || |||||||||||||| | || | |||||||||||||| |||||||| |||||||| ||| | || || || || ||||| |||||||||||| | ||| | |||| | |||| || | ||| ||| ||| | | || |||| | | || | |||||||| | | || |
GGATGCACTCCGATATCATAAGATTATTATTTTGACTGATGCTGATGTGGATGGTGCCCATATCCGAACTTTGCTACTGACATTTTTCTTCAGATATCAGgtaaagtatacacagcaaatgatgacaaaaggccaaaatctacacttacatggaagatgaaatccaagtcagctcctgtaagatataaatcaaaataaatgatcaaatttgatgcagtggttctttcttgcag
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA19G31030.1 (Glycine max), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtac-------------ttctaccctct-ttctgatactga---tcaaactggagttatggctgatctgttaggggccatcctaggtgttgcaacttcaaataa-attgttctctggt--
|| || || |||||||||||||| | || | |||||||||||||| |||||||| || ||||| || || || || || || ||||| |||||||||||| | ||| ||| ||| | | || | ||| ||| | || | || || || || | || || | | || | ||| |
AGATGCACTCCGATATCATAAGATTATTATTTTGACTGATGCTGATGTGGATGGTGCCCACATCCGAACACTGCTACTGACATTTTTCTTCAGATATCAGgtaaaatgatggcaaaatgctaaaatctactcttacatggaagatgaaaacctagtcggctcctataagatataaatcaaaataaatgatcaaatttgatgcagtgtttctttcttgcag
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT5G04130.1 (Arabidopsis thaliana), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctaccctctttctgatactgatcaaactggagttatggctgatctgttag--gggccatcctaggtgttgcaacttcaaataaattgttctctggt
||| | | || || ||||||||| |||| | || ||||| ||||| |||||||||||||||||||| ||||| | || || ||||| |||||||||||| | | || ||| |||| | | || | || | | | | |||| ||| | | | || || |||| |
AGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCTTTTTCTTCAGATATCAGgtattagt-------------taaggattaaacaaaaatatcccctaaatatttggcagagttaatctagttgtaaacatgacttaaaatttcttctacag-
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 5'ss of exon 18
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctaccctctt-tctgatactgatcaaactggagtt-atggctgatct-gttaggggccatcctaggtgttgcaacttcaaataaattgttctctggt
||| ||| || || ||||| || |||| | || ||||| ||||| |||||||||||||||||||| ||||| | || || ||||| |||||||||||||| | | | | | | | | || | | || || |||||| |||| | | || | | | | ||| |
GGAGAATCTGCGTTACCATAAAATTATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCTTTTTCTTCAGATATCAGgtactagtttagtttgataaaacattagttgaagtagccttgattgctgattgagttatgtgaaatttaatgaaatttactttctacag--------------
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttct----accctctttctgatactgatcaaactggagttatggctgatctgttaggggccatcctaggtgttgca-acttc---aaataaattgttctctggt-----------------
||||||||| || |||||||| || |||| | || ||||||||||| |||||||| |||||||| ||||| || | ||||| |||||||||||||||||| | | | ||| | | | | | | | | || || | | | | | || | | ||| |||||| | | | || |
GGAAGCTCTCCGTTATCATAAAATCATCATCTTAACAGATGCTGATGTGGATGGTGCTCATATCCGAACTCTGCTGTTGACTTTTTTCTTTAGATATCAGgtagatattggggagacttgtctcaaattatttatgtgaacataaagataaataagtcaaagcttcttcaaatgtttacttagttcgaaaaataatataatttatgctgtttttcttgctttcag
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S275_106V6.1 (Physcomitrella patens), 5'ss of exon 17
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttcta--ccctctttctgatactgatcaaactggagttatggctgatctgttaggggccat-cctaggtgttgcaacttcaaataaattgttctctggt------------------------------------------------------------------------------------
||| | | || || || |||||| | || || || ||||| ||||| |||||||| |||||||| || | || || || ||||||||||||||||||||| || | |||| || || | || ||| | | | | | ||| || | | || || | | || |
GGATTCATTGCGTTACCACAAGATAATTATTCTGACAGATGCGGATGTGGATGGTGCTCATATCCGCACCTTGCTTCTAACATTCTTCTTTAGATATCAGgtaattgagagtctctcttctaatccttgcttcttttctgtagcactgaggctgagctgaatcttatttcaatattgtaagct-gattatataatgcagtgttggaacaatgtatcatttgaataagaatgtcacctcaagtatattttggtaggtatttaactgtttggtttggcttgttaaacagMapped 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|33800991|gb|CF326369.1|CF326369EST: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAG AAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
genomic: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctac ... gtctatgcagAAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
EST:
gi|66923153|gb|CX110001.1|CX110001EST: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAG AAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGCGCCTCCTCTTTAC
genomic: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctac ... gtctatgcagAAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
EST:
gi|218495419|gb|FG960500.1|FG960500EST: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAG AAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
genomic: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctac ... gtctatgcagAAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
EST:
gi|89185707|gb|CI047576.1|CI047576EST: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAG AAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
genomic: ATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctac ... gtctatgcagAAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTAC
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:
64 (upstream exon),
54 (downstream exon)
Score:
24GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctac ... gtctatgcagAAAGCACTATTCGATGAAGGTTGCATTTATGTTGGTGTGCCTCCTCTTTACAAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTTTCTTCTTTAGATATCAGgtacttctaccctctttctgatactgatcaaactggagttatggctgatctgttaggggccatcctaggtgttgcaacttcaaataaattgttctctggt
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