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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttacttaggtttacctgtatgtcaagtattactactttcagtgtgtggtgtttgttgatgtgtatttgggtgttgcagtttttgctagtttttaa...

Basic information

species Zea mays
transcript GRMZM2G365035_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 9
GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgtt-----acttaggtttacctgta----tgtcaagtattactactttcagtgtgtggtgtttgttgatgtgtatttgggtgttgcagtttttgctagtttttaa
|||||||||||||||||||||||||||||||||||||||||||||||||||||  |||| || |||||||      ||||   ||  | |||      | |  |||||    | ||||  |    || ||  |  ||   | |||| ||   |  | |    |         
GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATTGTTGAGGCAgtatgttctcattcttataatttaccgtagtaacattatctattatcggtctcagattcacatgctttcttgtggtcacttggttggaactatgtgcaat---------
















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|149087834|gb|EE287144.2|EE287144
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|211142539|gb|FL467000.1|FL467000
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|32840606|gb|CD980287.1|CD980287
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTCTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|76017952|gb|DT945122.1|DT945122
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|149043308|gb|EE047371.2|EE047371
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|60345110|gb|DN212083.1|DN212083
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|22489585|gb|BU049508.1|BU049508
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|211516679|gb|FL422119.1|FL422119
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|76284446|gb|DV024014.1|DV024014
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|87153749|gb|DY398538.1|DY398538
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|32935092|gb|CF039904.1|CF039904
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGCCAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCCGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|18384244|gb|BM417443.1|BM417443
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|37388728|gb|CF631576.1|CF631576
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|33091766|gb|CF051760.1|CF051760
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|22489749|gb|BU049672.1|BU049672
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|32840607|gb|CD980288.1|CD980288
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|45567561|gb|CK985631.1|CK985631
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
EST: gi|149102041|gb|EE188040.2|EE188040
EST:     ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCG                         ATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA
genomic: ATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCA

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: 42 (upstream exon), 48 (downstream exon)
Score: 75

GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCAACACTACACGTGCATCAGCTGGTGGAACATGATACTGAGAAGTGGAAAT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 108

GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCAACACTACACGTGCATCAGCTGGTGGAACATGATACTGAGAAGTGGAAAT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 160

GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCAACACTACACGTGCATCAGCTGGTGGAACATGATACTGAGAAGTGGAAAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 81

GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttact ... tattgagcagATTGACAGTAATACAGATGGGCTAGTTGATTTTGAGGAGTTTGTTGCTGCAACACTACACGTGCATCAGCTGGTGGAACATGATACTGAGAAGTGGAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTTGCAAAGGATGTTCCATGGAGATTAAAGGGTCCACGTGTTTTAGAGATCATTGAAGCGgtatgttacttaggtttacctgtatgtcaagtattactactttcagtgtgtggtgtttgttgatgtgtatttgggtgttgcagtttttgctagtttttaa

- - - - - - - - -  CATGGA
- - - - - - - - - -  TGGAGA
- - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC