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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaaactgtttagtgcaattttttttccactgattatccaccaaagcagttttactttgatgatatatgaactcctaattgtttggttgcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT

Basic information

species Zea mays
transcript GRMZM2G053019_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053019_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 11
gaaaaaactgtttagtgcaattttttttccactgattatccaccaaagcagttttactttgatga-tatatgaactcctaattgtttggttgcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT
 || ||    | || |||||  || || |  |  ||| |  |  ||   | |   | |   ||||  ||||        |||   ||   || |||  |||||||||||||||||||||| ||||| || |||||||||||||||||||||||||| || ||||| ||||||||||||||||| || || ||||| |||||
-aacaattcatctattgcaaaattgttccatcgcattttgtaaaaagttattcaaattcaaatgagcatatatgacatcaatctattttgtgtttgctcagCGCAAGTTGGCATGACTCCAGAGGAGGTAGTATCGAAAATAATGGCAAACCCAGAAGTTGCTGTTGCATTCCAGAACCCAAAGATTCAAACAGCGATCAT
















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|13562296|gb|BG550516.1|BG550516
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|148929677|gb|EC876252.2|EC876252
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|71760741|gb|DR958678.1|DR958678
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|60339807|gb|DN206780.1|DN206780
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|78108044|gb|DV526462.1|DV526462
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|71440310|gb|DR821360.1|DR821360
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|13558181|gb|BG549537.1|BG549537
EST:     CCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: CCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|148986909|gb|EE030718.2|EE030718
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|86473951|gb|DY240321.1|DY240321
EST:     GCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: GCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|211123549|gb|FL444251.1|FL444251
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|149080111|gb|EE169130.2|EE169130
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|76292082|gb|DV031650.1|DV031650
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC
EST: gi|32800972|gb|CD953208.1|CD953208
EST:     TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTG                         CGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAAAGGCAAACC
genomic: TCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACC

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: 144

AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 169

AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

AAAGAACATGGGTGGATCTCCTGATCAATGGGATAACCGTATGCTTGATCACCTGAAGAACTTTGACCTTAGCAGTCCAGAAGTGCGGCAGCAGTTTGgtgagtgaat ... gcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcagttttactttgatgatatatgaactcctaattgtttggttgcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT
                             tcctaat  putative branch site (score: 227)
      ttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaaactgtttagtgcaattttttttccactgattatccaccaaagcagttttactttgatgatatatgaactcctaattgtttggttgcttgtacagCGCAAGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
gaaaaaa
- - - - - - - - - - - - - - ccactga
- - - - - - - - - - - - - - - - - - - -ccaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg