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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgctggctgcagataggactggtgtccactataatttggttatctagccctaagaatgccccatcagttgcttgttgttacggggctatgggc...

Basic information

species Zea mays
transcript GRMZM2G143330_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 5'ss of exon 2
CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgctggctgcagata-ggactggtgtccactataatttggttatctagccctaagaatgccc--catcagttgcttgttgttacggggctatgggc--
 ||||||||||| ||||||||||||||||| ||||||||| | |||||||| |||||||| ||||| |||||||| ||| | |||||||||||  ||||||||||   |  |  | |  ||  | ||| || || ||      |||||   |||   |||   ||  |    |  || |||||| || |     |  ||   |  
TGGCATCAAGGGGAGGATCAACAGGGCCGTGTGGGGGCCGTTGAACAGGACTATCATCACCGCCGGTGAGGATGCTACCATCCGCATTTGGGACACAGAGgttagctcg--gattacctatttgcactagt-tctaccgaccattggtg--ctacttctactcatcactagtactaggtgcttggtgctcgtcaggaatatacca

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 2
CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc--tggctgcagataggactggtgtccactataatttggttatctagccctaagaatgccccatcagttgcttgttgttacggggctatgggc----
 ||||||||||| ||||| |||||||| || ||||||||| | ||||||||||||||||| ||||| |||||||||||| | |||||||||||  | ||||||||  |||  |  |  ||  |     | || || ||||    | |      | |  |||  ||  |  |   |||     | |  |   |   |   ||     
TGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGATGCCACCATCCGCATTTGGGACACTGAGgttagcttgcatttacaacatttgcacatagt-tctactaaccatcg-----ttggtgctacaaactcatcgctagtactaggcttctggtgcttttcaggaatgc
















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|149043303|gb|EE047366.2|EE047366
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|101401501|gb|EB822430.1|EB822430
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAGGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|78119408|gb|DV537792.1|DV537792
EST:     CTATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|101401499|gb|EB822429.1|EB822429
EST:     CTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAGGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|211094201|gb|FL010324.1|FL010324
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|71440740|gb|DR821790.1|DR821790
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTTCTGAAAGAG
genomic: C-ATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTT-CTGAAAGAG
EST: gi|88751072|gb|DY535213.1|DY535213
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|31909181|gb|CD650790.1|CD650790
EST:     CCATCATCACTGCCGGAGAAGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCCGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|93283869|gb|EB676133.1|EB676133
EST:     CCATCATCACTGCCGGAGAGGATGC-ACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGAC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGAC
EST: gi|91872573|gb|EB402530.1|EB402530
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|78119407|gb|DV537791.1|DV537791
EST:     CTATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|148995509|gb|EE034699.2|EE034699
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|148930479|gb|EE285032.2|EE285032
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|78087877|gb|DV516270.1|DV516270
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|71301123|gb|DR786594.1|DR786594
EST:     CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAG                         ACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: CCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
EST: gi|71301121|gb|DR786593.1|DR786593
EST:     GGGATTCAGAG                         ACTGGACAATTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC
genomic: GGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACCATTTCATCATTGTCAAAATCCCTAGATTGGTCACATTTTATTACTGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACCATTTCATCATTGTCAAAATCCCTAGATTGGTCACATTTTATTACTGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACCATTTCATCATTGTCAAAATCCCTAGATTGGTCACATTTTATTACTGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgc ... ttgtgtgcagACTGGACAACTTCTGAAAGAGTCTGACAAGGAATCCGGACATCAGAAGACCATTTCATCATTGTCAAAATCCCTAGATTGGTCACATTTTATTACTGGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGATGCCACCGTTCGCATTTGGGATTCAGAGgttaggatgctggctgcagataggactggtgtccactataatttggttatctagccctaagaatgccccatcagttgcttgttgttacggggctatgggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG