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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatctttgctagcttaagctaagttccctgcaaagatgaaattttgttcatcacgattagaattcatcaagaagaacctttgaggctggaattgc...

Basic information

species Zea mays
transcript GRMZM2G104166_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104166_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g45670.1 (Oryza sativa), 5'ss of exon 5
GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatctttgctagcttaagctaagttccctgcaa---agatgaaatttt-gttcatcacgattagaattcatcaagaagaacctttgaggctggaattgc
||||||||||||||| || ||||| |||||||| |||||||| ||||| |||||| | ||||| ||||||||| ||| |||||||||||||||||| ||||||||    | |   |  || |  |||||  | |  |    | || | ||    |   ||  |  | |||  |  | |   || |  |||||  |   |     
GGCAGAGCCACTGCGAGCAATGGTCATGGGTGCGCCTTTAGAAGATGCGAGACATCTAGCCCAAAGATATGACCGAATGAGGCAAGAAGCTGAAGCCCAGgtgaagtagtgtataacttttacttaagtctcttcaaggttatataacatcccaggatattgctctcagatgtacttac--agcatatttgaaacaatatcc--
















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|91056507|gb|EB166925.1|EB166925
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|74236878|gb|DT644792.1|DT644792
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|148996413|gb|EE035708.2|EE035708
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|20301506|gb|BQ164449.1|BQ164449
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|76283090|gb|DV022658.1|DV022658
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|91873694|gb|EB403651.1|EB403651
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|148981761|gb|EE027867.2|EE027867
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|26456480|gb|CA828063.1|CA828063
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|148970807|gb|EE021570.2|EE021570
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
EST: gi|76927135|gb|DV171161.1|DV171161
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTA
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTA
EST: gi|93012221|gb|EB637741.1|EB637741
EST:     GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCCGAAGCACAG                         GCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT
genomic: GACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAAT

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: 40 (upstream exon), 49 (downstream exon)
Score: 68

GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAATGGCGATATGGTATCAAAATTGGAAGCTGCCGAGTACAAGCTTGAAGAAC


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 172

GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAATGGCGATATGGTATCAAAATTGGAAGCTGCCGAGTACAAGCTTGAAGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAATGGCGATATGGTATCAAAATTGGAAGCTGCCGAGTACAAGCTTGAAGAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatct ... ttctttttagGCTGTCGAAGTATCAAGACGGCAGAACAGGGTGAGGGAATCTACTGGGAATGGCGATATGGTATCAAAATTGGAAGCTGCCGAGTACAAGCTTGAAGAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAGAGCCACTGCGGGCGATGGTTATGGGTGCACCTTTAGAGGATGCCAGACATATGGCCCAGAGATATGACAGAACGAGGCAAGAAGCTGAAGCACAGgtgaacatctttgctagcttaagctaagttccctgcaaagatgaaattttgttcatcacgattagaattcatcaagaagaacctttgaggctggaattgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaagaa