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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctatagcattattatctgtatatagtttcattcagtggcatattattaagatggttgcataacgtgcaccaataattttaagcctacttgctgca...

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 10
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g39420.2 (Oryza sativa), 5'ss of exon 10
GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctatagcattattatctgtatatagtttcattcagtggcat-attattaagatggttgc--ataacgtgcaccaataattttaagcctacttgctgca
||||||||  |||||||| || ||||||||||||||||||||||| ||||| |||| |||||||||| |||||||  | ||||| ||||||||| |   ||| | ||   |  | | |  |||  |   ||  || |||    |  || |   ||   |  | || | |||       || || ||   
GGATAAAAATATAATAGGCAACGCGATCACTCCCTTCATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctacaaatttaatttcaa-actttgctgtattttgaaccacgatgattttcgtatttccctgtagttttgagcattgattagctatttattt-ctat-

upper sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g39420.1 (Oryza sativa), 5'ss of exon 9
--------------GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctatagcattattatctgtatatagtttcattcagtggcat-attattaagatggttgc--ataacgtgcaccaataattttaagcctacttgctgca
              ||||||||  |||||||| || ||||||||||||||||||||||| ||||| |||| |||||||||| |||||||  | ||||| ||||||||| |   ||| | ||   |  | | |  |||  |   ||  || |||    |  || |   ||   |  | || | |||       || || ||   
CTATGTTGTTTCAGGGATAAAAATATAATAGGCAACGCGATCACTCCCTTCATGCTTGACAGAGTGAAAGTACTAACTGGACGATCTTCGCTAGAAGCCAgtatcctacaaatttaatttcaa-actttgctgtattttgaaccacgatgattttcgtatttccctgtagttttgagcattgattagctatttattt-ctat-
















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|60347683|gb|DN214656.1|DN214656
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|211233176|gb|FL456644.1|FL456644
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|9255049|gb|BE345517.1|BE345517
EST:     GCTTGAAAGAGTAAAAGAACTATCCGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: GCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|8516322|gb|BE123048.1|BE123048
EST:     CATGCTTGAAAGAGTAAAAGAACTAACCGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|9255050|gb|BE345518.1|BE345518
EST:     AAAGAACTAACCGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: AAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|166684431|gb|EG202720.1|EG202720
EST:     AGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: AGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|71533571|gb|DR784330.1|DR784330
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACCTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|71764026|gb|DR961963.1|DR961963
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|211233175|gb|FL456643.1|FL456643
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATYTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|88748923|gb|DY533064.1|DY533064
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|74236391|gb|DT644305.1|DT644305
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|149082842|gb|EE172068.2|EE172068
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
EST: gi|211420627|gb|FL480892.1|FL480892
EST:     CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTA                         ATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG
genomic: CATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTG

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: 46 (upstream exon), 48 (downstream exon)
Score: 55

GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 62

GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 71

GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCA


Block sizes: 43 (upstream exon), 39 (downstream exon)
Score: 28

GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctata ... tgatgtttagATATTGCACTTGTTAAGAACAATGCTCTTATTGGTGCGAACATTGCTGTTGCCCTTTCTAACCTTCAGCAGAGAGAAATAAGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAAAAGGATAATAGGAAATGCGATCACTCCCTTCATGCTTGAAAGAGTAAAAGAACTAACTGGAGGATCTTCCTTGGAAGCTAgtatcctatagcattattatctgtatatagtttcattcagtggcatattattaagatggttgcataacgtgcaccaataattttaagcctacttgctgca

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG