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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctttgtttctttataactagtcccgtttgttttgtgggtttttccctcctatttttgaaaaaagttttaagatctttgctctctttgctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 6
ctcctttgtttctttataactagtcccgtttgttttgtgggtttttccctcctatttttgaaaaaagttttaagatctttgctctctttgctct-tgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA
|   ||  ||||  | | |  ||| |  |||      ||   | |||||| ||            |  |||||  |   ||  | || |      ||  ||||||||||| ||||| ||||||||||| || |||||||||||||||||||| ||||| || |||||||| |||||||||||| | ||||| ||||| |||
caagttcatttcactctcaagagttct-tttaggccatgctatcttccctgctgaaagaaggctgatgtttaatcttcatgaaccctgtatcaaatgatagGTTGAACAAGACACCCCCCAATTTGACATTTAGAAGAAAGGACAAGGGTGGCATCAATTTTACATCAACTGTGACGAACACAAACTTGGATCTTGAAACA
















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|32836870|gb|CD976548.1|CD976548
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32837261|gb|CD976939.1|CD976939
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|71769273|gb|DR967210.1|DR967210
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32919863|gb|CF024675.1|CF024675
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCA
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCA
EST: gi|32839263|gb|CD978944.1|CD978944
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32848352|gb|CD988033.1|CD988033
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|67034867|gb|CO463400.1|CO463400
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|60353675|gb|DN220648.1|DN220648
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|74240038|gb|DT647952.1|DT647952
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGA
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGA
EST: gi|14203739|gb|BG837416.1|BG837416
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|71418217|gb|DR804368.1|DR804368
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|76937221|gb|DV175090.1|DV175090
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|71436936|gb|DR817986.1|DR817986
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32836351|gb|CD976029.1|CD976029
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|67042509|gb|CO468764.1|CO468764
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|22542064|gb|BU092502.1|BU092502
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|33094247|gb|CF054241.1|CF054241
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32836178|gb|CD975856.1|CD975856
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|87155566|gb|DY400355.1|DY400355
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|71312952|gb|DR792998.1|DR792998
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|74233974|gb|DT641888.1|DT641888
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAGAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|60343127|gb|DN210100.1|DN210100
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|6527040|gb|AW216258.1|AW216258
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTC
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTC
EST: gi|60353517|gb|DN220490.1|DN220490
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAG                         GTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGG
EST: gi|32836350|gb|CD976028.1|CD976028
EST:     ATAACTCACAAGCGTCTTATTGAGAAGGAGCCTGAAGGATTTGGCATTAG                         GTTGAACAAAACA
genomic: ATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACA

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), 45 (downstream exon)
Score: 211

CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 160

CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 143

CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttc ... ctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctcctatttttgaaaaaagttttaagatctttgctctctttgctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA
                              tctttgctctctttgc  CT-rich tract
       tatttttgaaaaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctttgtttctttataactagtcccgtttgttttgtgggtttttccctcctatttttgaaaaaagttttaagatctttgctctctttgctcttgtcagGTTGAACAAAACACCACCCAATTTGACTTTCAGAAGAAAGGACAAGGGTGGAATCAACTTCACATCAACAGTGACGAACACACATTTGGACCTTGATACA

- - - tgtttct
- - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa