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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctttccaaaatcgtatattaacgcatctaagtcagaaaggaatgaaagaatgacgaattcaaatggataaaaaaatatatgctcacatcttttgaagtgacatagtgcaaccaatctaaggtatgtgcctggagttcacctgttgcttttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG

Basic information

species Zea mays
transcript GRMZM2G051842_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 6
gtgagtctttccaaaatcgtatattaacgcatctaagtcagaaaggaatgaaagaatgacgaattcaaatggataaaaaaatatatgctcacatcttttgaagtgacatagtgcaaccaatctaaggtatgtgcctggagttcacctgttgcttttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG
                                                                | | |     |      |||    ||| || || |  |||||    |||  ||| || ||  |||| |  |||  ||   | ||||  ||       ||||||||  |||  ||  |||||||||||||| ||||| ||||||| |||||| || |||||||| ||||| || || ||||| ||||||||||| || |||
---------------------------------------------------------------gtgataccctcatcgccttattgtttcagatgttcttcagtga----gtgatacctat-tatagtatat--ctgatgtgtgcgtgtttttt-------cagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG
















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|29576892|gb|CB617004.1|CB617004
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|29543849|gb|CB604229.1|CB604229
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|31612067|gb|CD568689.1|CD568689
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|29945521|gb|CB815681.1|CB815681
EST:     GAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: GAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|29945789|gb|CB815820.1|CB815820
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|148928772|gb|EC873535.2|EC873535
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|71762333|gb|DR960270.1|DR960270
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|78103938|gb|DV522356.1|DV522356
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|211123067|gb|FL031406.1|FL031406
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|29543893|gb|CB604273.1|CB604273
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTTTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|60338856|gb|DN205829.1|DN205829
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|101385265|gb|EB814678.1|EB814678
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
EST: gi|30032244|gb|CB834095.1|CB834095
EST:     AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG                         GGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA
genomic: AACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 13

ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtgagtcttt ... ttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcaaccaatctaaggtatgtgcctggagttcacctgttgcttttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG
                                          cttttatct  CT-rich tract
                                           ttttatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctttccaaaatcgtatattaacgcatctaagtcagaaaggaatgaaagaatgacgaattcaaatggataaaaaaatatatgctcacatcttttgaagtgacatagtgcaaccaatctaaggtatgtgcctggagttcacctgttgcttttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG