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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagcaaatggcttcttaatctgctagtacatgattggtattttcttagaacaagaatgaaaaaggagccgactcttacattgtgtgcttttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 1
ctagcaaatggcttcttaatctgctag--tacatgattggtattttcttagaacaagaatgaaaaag--gagccgactcttacattgtgtgcttttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC
     | |  |  | | |||||||||   | ||| | |  | || | ||||||  |    ||||      |    | ||      |       ||||| ||||||||||||||| || | |||||| || ||||||||||||||||||||||| ||||| || || |||||||| |||||||||||||| |||||||| |||||
----aatagagtatttaaatctgctactttgcattacttttgttctattagaaggatggcgaaaggacttaattaaatccgttgctcctgaaatttgaaaacagAGGTGAAGGCGTCTGCAAATGTATTTGGGAACTACTTCCAGGTTGCAACTTATGGAGAGTCTCATGGAGGCGGTGTTGGTTGCGTAATCAGTGGATGCCC
















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|211165638|gb|FL126857.1|FL126857
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGCGCCTCCAGCCTAG                         AGGTGAAGGCATCAGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165636|gb|FL126855.1|FL126855
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGCGCCTCCAGCCTAG                         AGGTGAAGGCATCAGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|149088514|gb|EE177624.2|EE177624
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|28361588|gb|CB239944.1|CB239944
EST:     ACGTCCCTCCGGCTATCCGTCGGCCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: ACGTCCCTCCGGTTATCCGTCGG-CCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165635|gb|FL126854.1|FL126854
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165641|gb|FL126860.1|FL126860
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165634|gb|FL126853.1|FL126853
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGMCGTCGCCGCGCCTCCAGCCTAG                         AGGTGAAGGCATCAGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062099|gb|FL126842.1|FL126842
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062097|gb|FL126840.1|FL126840
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165637|gb|FL126856.1|FL126856
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165632|gb|FL126851.1|FL126851
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062105|gb|FL126848.1|FL126848
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGCGCCTCCAGCCTAG                         AGGTGAAGGCATCAGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062104|gb|FL126847.1|FL126847
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGCGCCTCCAGCCTAG                         AGGTGAAGGCATCAGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|37424877|gb|CF650172.1|CF650172
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062107|gb|FL126850.1|FL126850
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211062101|gb|FL126844.1|FL126844
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165640|gb|FL126859.1|FL126859
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|149100015|gb|EE186068.2|EE186068
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
EST: gi|211165639|gb|FL126858.1|FL126858
EST:     CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAG                         AGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT
genomic: CACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCT

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: 125

TCCACACGGTTTCTCCCCCGCGGGATAGGCGCGCTCCCGGAGTCCGCTCCCACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

TCCACACGGTTTCTCCCCCGCGGGATAGGCGCGCTCCCGGAGTCCGCTCCCACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

TCCACACGGTTTCTCCCCCGCGGGATAGGCGCGCTCCCGGAGTCCGCTCCCACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 446

TCCACACGGTTTCTCCCCCGCGGGATAGGCGCGCTCCCGGAGTCCGCTCCCACGTCCCTCCGGTTATCCGTCGGCCGCCGTCGCCGGGCCGCCAGCCTAGgttcgcctgg ... ttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaacaagaatgaaaaaggagccgactcttacattgtgtgcttttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC
                           ctcttac  putative branch site (score: 446)
                                        tgctttt  putative PPT
          aatgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagcaaatggcttcttaatctgctagtacatgattggtattttcttagaacaagaatgaaaaaggagccgactcttacattgtgtgcttttgagaacagAGGTGAAGGCATCGGGAAATGTGTTCGGGAACTACTTCCAGGTTGCAACCTATGGCGAATCCCATGGAGGGGGTGTTGGTTGCGTTATCAGTGGCTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - -ggcttct
- - - - - - - - - -tctgcta
- - - - - - - - - - - - - gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - -aacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgctt