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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccctgtagaaactcatcccacctactatactgctttagtcatttgagtcttcctgacatggtgccatcttgacgcag

Basic information

species Zea mays
transcript GRMZM2G053019_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053019_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 5'ss of exon 12
AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccctgtagaaactcatcccacctactatactgctttagtcatttgagtcttcctgacatggtgccatcttgacgcag
||||||||||||||| ||||| || |||||||||||||||||||||||||| || ||||| ||||||||||||||||| || || ||||| |||||||| |||||   ||||| ||| ||||  ||  ||||  |      ||  |  |||  ||||| | |||  |   |||||||| ||||
AGTTGGCATGACTCCAGAGGAGGTAGTATCGAAAATAATGGCAAACCCAGAAGTTGCTGTTGCATTCCAGAACCCAAAGATTCAAACAGCGATCATGGATgtaagtttctgtacaaattcatttcat-tactgaa------taaactgttgcatcttc-taacaaagaatcatcttgatgcag
















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:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|148929677|gb|EC876252.2|EC876252
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|71760741|gb|DR958678.1|DR958678
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|60339807|gb|DN206780.1|DN206780
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATAATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|78108044|gb|DV526462.1|DV526462
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|71440310|gb|DR821360.1|DR821360
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|13558181|gb|BG549537.1|BG549537
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|148986909|gb|EE030718.2|EE030718
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|86473951|gb|DY240321.1|DY240321
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|110518254|gb|EE022841.1|EE022841
EST:     CCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: CCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|211123549|gb|FL444251.1|FL444251
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|149080111|gb|EE169130.2|EE169130
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|91051305|gb|EB161723.1|EB161723
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|76292082|gb|DV031650.1|DV031650
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG
EST: gi|32800972|gb|CD953208.1|CD953208
EST:     ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGAC                         TGCTCGCAGAACCCTCTTA
genomic: ATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTA

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), 48 (downstream exon)
Score: 114

AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 208

AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 111

AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 124

AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccct ... cttgacgcagTGCTCGCAGAACCCTCTTAACATTGTAAAGTACCAAAACGACAAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGCATGACTCCCGAGGAAGTGGTATCGAAAATAATGGCAAACCCAGATGTAGCTGTCGCATTCCAGAACCCAAAAATACAGACAGCCATCATGGACgtaagaccctgtagaaactcatcccacctactatactgctttagtcatttgagtcttcctgacatggtgccatcttgacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA