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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtacttgatgtttcatggattaaatatacccccacattgatttcagttccaatcaggaacatttgaacaaacaaaacatattcaataggcattaga...

Basic information

species Zea mays
transcript GRMZM2G451366_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 5'ss of exon 8
GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtacttgatgtttcatggattaaatatacccccacattgatttcagttccaatcaggaacattt---gaacaaacaaaacatattcaataggcattaga
|| || || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| | |||||     |  |  |   | ||||      ||||  ||    ||   |   |  |   |    | ||  ||| || ||||| | |   | |||  
GATTTCTCTGATGTCTCTAAAGAGATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGGgtatgcacttgtcacctttttaaa-gagtatatattaccattagttctgattaggaatggacatggtgatggtacccacataatatattta-tgatccttat-
















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|32847269|gb|CD986950.1|CD986950
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACCACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAA-CACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
EST: gi|32841613|gb|CD981294.1|CD981294
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|211499698|gb|FL406841.1|FL406841
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTATA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32840746|gb|CD980427.1|CD980427
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|89252033|gb|DY623819.1|DY623819
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32841252|gb|CD980933.1|CD980933
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32839985|gb|CD979666.1|CD979666
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32839499|gb|CD979180.1|CD979180
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32839696|gb|CD979377.1|CD979377
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32840986|gb|CD980667.1|CD980667
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACCACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAA-CACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
EST: gi|32841122|gb|CD980803.1|CD980803
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCA
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCA
EST: gi|32841145|gb|CD980826.1|CD980826
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACCACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAA-CACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTAC
EST: gi|211532947|gb|FL381078.1|FL381078
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32840104|gb|CD979785.1|CD979785
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAACGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32840762|gb|CD980443.1|CD980443
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32863734|gb|CF003416.1|CF003416
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32841116|gb|CD980797.1|CD980797
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32841526|gb|CD981207.1|CD981207
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|32945502|gb|CF050321.1|CF050321
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACT
EST: gi|61119699|gb|DN560660.1|DN560660
EST:     GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA                         GTAGCATGGGAACACGAACAGTT
genomic: GTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTT

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: 154

GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACTCTTTCAGAAATGTCTACCCCTCCTGAATTTTTGGAAAGCACTGGTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACTCTTTCAGAAATGTCTACCCCTCCTGAATTTTTGGAAAGCACTGGTGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACTCTTTCAGAAATGTCTACCCCTCCTGAATTTTTGGAAAGCACTGGTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtactt ... aaacttgcagGTAGCATGGGAACACGAACAGTTCTCGAGGTTTAGAGTGACCGCACTTACTCTTTCAGAAATGTCTACCCCTCCTGAATTTTTGGAAAGCACTGGTGGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGAgtacgtacttgatgtttcatggattaaatatacccccacattgatttcagttccaatcaggaacatttgaacaaacaaaacatattcaataggcattaga

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaaa