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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtattgtgagga...

Basic information

species Oryza sativa
transcript LOC_Os02g52140.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G862331_T04 (Zea mays), 5'ss of exon 2
------------GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtattgtgagga
            ||| |||||||||| |||||||||||||||||||| || ||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||   ||||||||   ||  |||    |||  ||||||||    | |    || ||||| | || |  | |   ||     |  |||||| ||   | |     
CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgttgtcttccta-tgtgctca---cccaccttgccttt-ttgatgctt----gataccttttttgcggtgtgtttaggtttcattattatggttcgatatgctatatac---

upper sequence: LOC_Os02g52140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G108919_T03 (Zea mays), 5'ss of exon 2
------------GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtattgtgagga
            ||| |||||||||| | |||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||    || |||   |||  |||    ||| | |||||||                                                                
CTTCAGGAGCTTGACGAGATGAAGCGCAAGCTGAAGGAGATGGAGGaggaggccgccgccctccgcgatatgcaggccaaggtcgccaaggagatgcaaggttgtcttccta-cgtactc---gcccaccttgccttttc-gatgcttggt-------------------------------------------------------------

upper sequence: LOC_Os02g52140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G108919_T02 (Zea mays), 5'ss of exon 2
------------GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtattgtgagga
            ||| |||||||||| | |||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||    || |||   |||  |||    ||| | |||||||   ||||||     ||||  | || |  | |   |   |     |||||  | |  | | ||  
CTTCAGGAGCTTGACGAGATGAAGCGCAAGCTGAAGGAGATGGAGGAGGAGGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgttgtcttccta-cgtactc---gcccaccttgccttttc-gatgcttg-gtgttttc----ttgcagtgtgttgaggtttcactagagcggttcga--tatgctataagcc

upper sequence: LOC_Os02g52140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S3_616V6.1 (Physcomitrella patens), 5'ss of exon 2
---GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCG---CCGGgtgtgctcactgcctgcctaatttttactg-atgcttttatgtttttcttgttgcgatctgctatgttcatatcg--gcctcattcgatctgtattgtgagga
   ||  ||||||||  | |  ||||||||||||||||||||||||| || || || || ||||| || || || |  || ||||||   ||| |||       |  |   |  |||  ||  |  ||||  | |          ||   |||    ||   |  | | |  |  | |  |  ||  ||||     |||||        
CTGGAGGAGATGAAGAAACGTTTGAAGGAGATGGAGGAAGAGGCCGCTGCTCTACGTGATATGCAAGCTAAAGTTGAGAAAGAGATGGGTGGTAGTCAAGgtttgaatcctcctactcgctctcgcatttcaattctgcatagcaattagtttggctttaaaacttaccaactctaaaaggatgctgcattta---tgtatca------

upper sequence: LOC_Os02g52140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 5'ss of exon 2
---GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtat-tgtgagga-
   ||  ||||||||  | |  ||||||||||||| ||||| || || || || |||||||||||||| || ||||  |||||||||   ||| |||     ||| || |   | | |   || | |    || |   ||          |      ||| |   ||    | || |   |   |  || | | |   | |    
CTAGAGGAGATGAAGAAACGCTTGAAGGAGATGGAAGAAGAAGCTGCTGCTCTGCGCGACATGCAGGCTAAAGTCGAGAAGGAGATGGGCGGTAGTCAA---Ggtttgatt-tttcttatttactctcgcatgttaacttcgcacagcagtaagcctgattttgaat-cagaaattgatttttctttatgtttttacataaccga

Mapped 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|88294313|gb|CI667287.1|CI667287
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|58682534|gb|CK071221.1|CK071221
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88326040|gb|CI651090.1|CI651090
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|41883257|gb|BX928330.1|BX928330
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|32948090|gb|BP184662.1|BP184662
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAA------------G                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88391254|gb|CI595508.1|CI595508
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTAAAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88334791|gb|CI647173.1|CI647173
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|32948232|gb|BP184804.1|BP184804
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAA------------G                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88306219|gb|CI636603.1|CI636603
EST:     CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: CCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC

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: 62 (upstream exon), 73 (downstream exon)
Score: 58

GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcac ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTCGATCTGTGTATGTTGGAAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGGTGGTCCGCCGGgtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatctgtattgtgagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG