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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattcttcagactagttaacagttgcttatctgcattgagtgcatgcatgctatgctagtgtgagaacattgcttatatagttcttgctggttaaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G063192_T01
intron # 4
splice site 3'
intron type U2

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|37394528|gb|CF634540.1|CF634540
EST:     GGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         TGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: GGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|110202735|gb|EC884632.1|EC884632
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTTTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|149095468|gb|EE181116.2|EE181116
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|149100953|gb|EE187050.2|EE187050
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTTTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|110200330|gb|EC882227.1|EC882227
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTTTTCATGGTTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|110208507|gb|EC890404.1|EC890404
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60339227|gb|DN206200.1|DN206200
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|93283041|gb|EB675305.1|EB675305
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60355229|gb|DN222202.1|DN222202
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|148951592|gb|EC897327.2|EC897327
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTTTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|4621663|gb|AI612496.1|AI612496
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|211094285|gb|FL471105.1|FL471105
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|88750043|gb|DY534184.1|DY534184
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGTTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60356758|gb|DN223731.1|DN223731
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60397177|gb|DN229993.1|DN229993
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60354385|gb|DN221358.1|DN221358
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60342791|gb|DN209764.1|DN209764
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|83279260|gb|DV943268.1|DV943268
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60343232|gb|DN210205.1|DN210205
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|4225449|gb|AI395902.1|AI395902
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|149113104|gb|EE295867.2|EE295867
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|60337787|gb|DN204760.1|DN204760
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|110946074|gb|EE166231.1|EE166231
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|149043944|gb|EE047425.2|EE047425
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|16926664|gb|BM079732.1|BM079732
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|211006919|gb|FL435027.1|FL435027
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
EST: gi|16926133|gb|BM079201.1|BM079201
EST:     AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAG                         AGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG
genomic: AGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGG

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: 284

TGGATTCACACAGAACCAACTCACCTTGTGGAAGTACCCATCGATGGTGAAGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 16

TGGATTCACACAGAACCAACTCACCTTGTGGAAGTACCCATCGATGGTGAAGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 25

TGGATTCACACAGAACCAACTCACCTTGTGGAAGTACCCATCGATGGTGAAGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 19

TGGATTCACACAGAACCAACTCACCTTGTGGAAGTACCCATCGATGGTGAAGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattct ... taaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctatgctagtgtgagaacattgcttatatagttcttgctggttaaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG
                          ttatatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattcttcagactagttaacagttgcttatctgcattgagtgcatgcatgctatgctagtgtgagaacattgcttatatagttcttgctggttaaactgcagAGTCCTGATGGATGCACAGTAGCGTCGGCTGCTGCTGACGAGACCCTCCGGTTCTGGAACGTTTTTGGAACCCCTGAAACGCCCAAGCCTGCAGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG