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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccctacttgacaacctttttcttgaaccattatactcttgtgatcaactgtagttggcctggttacttactatagaaaaatgcaatgctaaaga...

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 6
GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccctacttgacaacctttt--tcttgaaccattat-actcttgtgatcaactgtagttggcctggttacttactatagaaaaatgcaatgctaaaga
||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||| |||||||| |||||||||  |||| |   || |  | |  | | |   |  | | ||| | || |||||||     ||| |||   | ||| |   
GGAGGTGGAAGATCATCAGCAAGAGAGACCATTGGAAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTTAAGCTCAAATCTGGAGTAGAGgtgtgatcctacttggcaaccttttactcttaactgatcaagatttgtatcaagcatcgcaattgacatgtttacttatccatgaacaattggacgctga---

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 5'ss of exon 6
GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccctacttgacaacctttttc--ttgaaccattatactct-tgtgatcaactgtagttggcctggttacttactatagaaaaatgcaatgctaaaga--------
|| ||||||||||| ||||| |||||||||||||  || || ||||| |||||| | ||||||||||| || |||      || ||   |||||||||       || |  | |||| ||  |  || |||| |  |    || ||||  || |||||   |  ||||  |   || ||      | | ||| | |        
GGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAGgtgtg-------tttatgatctttgtcactgaaatcattctttttaacgttatca--tgaagttg-tatttttacacaaactataatttctgagttctacaaaatgatcag
















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|149088514|gb|EE177624.2|EE177624
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTG
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTG
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAGATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTG
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTG
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CTGCAGGAGCTCTTGCAA-GAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTT
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTT
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG                         ATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA
genomic: CTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCA

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: 152

GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 422

GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 383

GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 429

GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccct ... ctacatgcagATCTTGGCATTTGTTTCTAAAGTGCACCAAGTCGTACTTCCAGAAGATGCAGTTGATTATGAGACTGTAACCTTGGAACAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAGgtgtgaccctacttgacaacctttttcttgaaccattatactcttgtgatcaactgtagttggcctggttacttactatagaaaaatgcaatgctaaaga

- - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagaaaaa