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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG

Basic information

species Zea mays
transcript GRMZM2G443985_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 13
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagc--at-ctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG
                          | | |  ||||  | ||  ||| | |   | || |   || |  | |   |   | ||||||    | | ||| |||| |||| |||  | |    || |   | |   |||||||||| |||||||||||||||| |||||| || || || |||||||||||||| |||||||| || || ||||||||||| |||||  |||| ||||  |
--------------------------gtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgct----ccactgctctccatactgattactgtcttatcactaaaatt--ttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCAAGACTTCTCTCCTCAACCAACCAGCCAAGTTTCCTCAGCAAGAAAGATG

upper sequence: GRMZM2G443985_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactc----acttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG
                                    | |  ||| |   ||||||  | | ||||   |    | | ||  | ||   |  |      ||  || ||    ||||   |   | ||| |       | ||||||||||| ||||| ||||||   ||   ||| || |||||||||||||||||||| ||||| ||||| |||||||| || ||| |  ||  |||||  |
------------------------------------catcatactg---tcatcag-ttatcatcaccgttaaagtcatcatcctcatatcatcataatc-atagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

upper sequence: GRMZM2G443985_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG
                               |||||| |  |  | |  || | |    |  || |    | ||  | ||      ||||   ||   |   ||| ||   ||||| ||| |  | |    |   || | || |  ||||  | |||||  |||  ||||||||||||||||||||||||||| || ||||| || ||||||||||||||||    |  |||||  |
-----------------------------aagaattcatggtgtc-ctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggt---tacaaaac-ttttgtatttgactgatgtgc---agCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

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|33098292|gb|CF058252.1|CF058252
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|16379999|gb|BI993250.1|BI993250
EST:     TTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: TTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|32857486|gb|CD997167.1|CD997167
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTTCATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|91872759|gb|EB402716.1|EB402716
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|5597293|gb|AI891391.1|AI891391
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|211018810|gb|FL462120.1|FL462120
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGBTACATCCCATTCTAT                         AGAATAMCAGAGAAGCAGAMCAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|148972519|gb|EE023480.2|EE023480
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|33285656|gb|CF075451.1|CF075451
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|32938726|gb|CF043545.1|CF043545
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|32940332|gb|CF045151.1|CF045151
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|33097586|gb|CF057546.1|CF057546
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|5895959|gb|AW037205.1|AW037205
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|148982504|gb|EE028349.2|EE028349
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|5740308|gb|AI947998.1|AI947998
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|14244950|gb|BG842888.2|BG842888
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|76016085|gb|DT943255.1|DT943255
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|33097989|gb|CF057949.1|CF057949
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|6020683|gb|AW065491.1|AW065491
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGG
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGG
EST: gi|88747280|gb|DY531421.1|DY531421
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|78022684|gb|DV491071.1|DV491071
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
EST: gi|5325011|gb|AI783202.1|AI783202
EST:     GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTAT                         AGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA
genomic: GTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCA

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: 116

CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 115

CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcaca ... ctcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG
                                             ctcacttc  CT-rich tract
                       taattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT