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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcacactttcaatggatccatccatttctttgtggtttctgtttgttttcatccatctgaaactcttgccttctaatgctttgtacaaacagagacatctgaatctgcctcattattttcgtaggccatataacaatcattagttttcttactttatatggtttctgtatatttccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 10
gtattcacactttcaatggatccatccatttctttgtggtttctgtttgttttcatccatctgaaactcttgccttctaatgctttgtacaaacagagacatctgaatctgcctcattattttcgtaggccatataacaatcattagttttcttactttatatggttt--ctgtata--------tttccatttt-cagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG
                       | |  ||   || |  ||| | | || |  ||     ||||     | |  |     || ||   ||||  | || ||  |   | || |  ||  || | ||    ||    |  |   ||    | || |||||  ||||  |   |||| |        | | |||  | ||||||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| || || ||||| || || | ||| ||||| || ||  |||| || 
---------------------gtaactcttctgttattatttttctctgctcccaaattgctga-----tggtttcaatgtgattcaaacaataacaggcagttt--tgtgtcctatatttcttgtttctcagtgcattagtgttttcctcctaactttg-atggcctgattgtaaaaatattgttctgcatgatgcagGTACCATGTTACAAATTTCTTTGCACCTAGCAGCCGATTTGGAACTCCAGAGGAACTTAAGTCTCTGATAGACAGAGCCCATGAACTGGGTCTGCTTGTT

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattcac--actttcaatggatccatccatttctttgtggtttctgtttgttttcatccatctgaaactcttgccttctaatgctttgtacaaacagagacatctgaatctgcc--tcattattttcgtaggccatataacaatcattagttttcttactttatatggtttctgtatatttccatttt-----cagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG
||||||    |   | | ||    |    |   |  |  | | | ||  | |  | ||   |    |||| |   ||| ||   |||||||| |     |  | ||| |||| |     | || |    |||   ||||  ||||  ||| |  | || |||  |  ||    ||   ||||| ||| |     |||||||||||| || || |||||||||||||| || || | |||||| |||||||| |||||||| || || |||| ||| || ||| | ||| || |||| 
gtattcttttaaccttagtgagctctagtagaacccta-gatatttgcatttaattattgttgcagaactatacgcttttaggcctttgtacca-tgatgctagctgtatcttcaagcaactagtagtatag---atatctcaattcttattggtttttcttactgaggaacatggccatttctattatgaatgcagGTACCATGTCACAAACTTTTTTGCCCCAAGCAGTCGCTGTGGGACCCCAGAGGAACTAAAATCACTGATAGATAGAGCTCACGAGTTAGGCCTGGTAGTT
















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|211263679|gb|FL032932.1|FL032932
EST:     GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGG                         GTACCATGTTACGAA
genomic: GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAA
EST: gi|87155797|gb|DY400586.1|DY400586
EST:     GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGG                         GTACCATGTTACGAANNNNNNNGCCCCAAGTAGCCGTTTTGGGACTCCAG
genomic: GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAG
EST: gi|26558524|gb|CA830759.1|CA830759
EST:     GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGG                         GTACCATGTTACGAA
genomic: GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAA
EST: gi|67022129|gb|CO450878.1|CO450878
EST:     GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGG                         GTACCATGTTACGAANNNNNNNGCCCCAAGTAGCCGTTTTGGGACTCCAGA
genomic: GCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGA

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: 1116

CTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 17

CTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

CTAACTTCAGAGATGAGGTGCTTCCAAGAATTAAAAAGCTTGGATACAATGCAGTACAGATAATGGCAATCCAGGAACACTCTTATTATGCAAGCTTTGGgtattcacac ... ccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacaatcattagttttcttactttatatggtttctgtatatttccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG
                ttcttac  putative branch site (score: 438)
                                          tttccattttc  putative PPT
         attagttttcttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcacactttcaatggatccatccatttctttgtggtttctgtttgttttcatccatctgaaactcttgccttctaatgctttgtacaaacagagacatctgaatctgcctcattattttcgtaggccatataacaatcattagttttcttactttatatggtttctgtatatttccattttcagGTACCATGTTACGAATTTTTTTGCCCCAAGTAGCCGTTTTGGGACTCCAGAGGACCTAAAATCTCTTATTGATAAAGCGCATGAGCTTGGCTTGCTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT