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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtactactccctccatttcaaaatgtagggcatattaggacttaaaaagtcaaacattttaaaatttgaccatcaattagccaaaatttctgtat...

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 5'ss of exon 7
GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtactactccctccatttcaaaatgtagggcatattaggacttaaaaagtcaaacattttaaaatttgaccatcaattagccaaaatttctgtat---
|| || ||| | || || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||||||||    | ||| | |  |  |  |||  |     |||        | |  |   || | |  ||    |||   |||  | ||   || | || | ||   
GATTTTCGATTGCGTGATATCAATGAGTACGCTGAGTGGTATGGCCATTCTCATAGGGCACCAGAACTTCAGgttttcctcgactacttaaacctagaaacctttttaataactaccgctgattatgtaatcgtgctattccttg--tatctttaagttcaa-tctcagcatgga

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 5'ss of exon 7
GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttc-----gtactactccctccat-----ttcaaaatgtagggcatattagg-act--taaaaagtcaaacattttaaaatttgaccatcaattagccaaaatttctgtat---------------------------------------------------------------------------------
|| |||||  | || || ||||||||||| |||||||||||||| ||| | || |||||||| |||||||||||||       |||   ||||| |||     || |     | | |    ||| | |||  ||  |  |  || || || |  | | | | |   |||   |  ||||   | |                                                                                 
GATTTCCGTTTGCGTGATATCAATGAGTACGCTGAGTGGTATGGTCATGCACATAGGGCACCAGAACTTCAGgttttcctggctacctgtccctacatacttgtttagttattggtgttggttatgcacttctactatttataagatctttagttctcagcgttgttta-tgagcatttgcttttagtaagatcttaagttatgtatcattaaattatgtttgtttatgaactcatactctgtggcttgcttctctgtttattcag
















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|78093374|gb|DV521748.1|DV521748
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|31354246|gb|CD438603.1|CD438603
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTAT
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTA
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTA
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACA
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACA
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     ATGAGTATGCTGAGTGGTATGGACATTCCCACATGGCACCGGAACTTCAG                         GGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT
genomic: ATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAAT

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: 220

GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAATGCACGCCTGGTAGCAAATCCAGGGTGTTATCCCACATCTATTCAACTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAATGCACGCCTGGTAGCAAATCCAGGGTGTTATCCCACATCTATTCAACTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAATGCACGCCTGGTAGCAAATCCAGGGTGTTATCCCACATCTATTCAACTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtact ... cacctttcagGGGGAAGCTGTGTATGGTTTGACCGAACTTAAACGAGATGACATAAGAAATGCACGCCTGGTAGCAAATCCAGGGTGTTATCCCACATCTATTCAACTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAGgtttcgtactactccctccatttcaaaatgtagggcatattaggacttaaaaagtcaaacattttaaaatttgaccatcaattagccaaaatttctgtat

- - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctcc