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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaccaaaaaagcttacatcgtcggtgttctgtgtacaataaatttcaattgtgtttctgaatttaagcccacatttcacatttcatcgtcgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------gcaccaaaaaagcttacatcgtcggtgttctgtgt-acaataaatt--tcaattgtgtttctgaatttaag--------------cccacatttcacatttcatcgtcgcattt-cagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC
                                                                          |     |||||| |   ||| | | | | |||| | |   |  |||  |   |||| ||| | ||   |||               |  |  |||  || | |   ||   ||| ||||||| || |||||||| ||||||||||||||||| |||||| || |||| || ||||| ||||||| |||||| ||||| ||||||||||||||||||||
gtctgtgatccttctccctaagcagaatacattgccggttaagttttttaaaattttctatgggatagaaaccagtggggaaaaagatggaatctttgatatgctgtatgattgttgattagttctttgtttttttaaaaaaaaggagtattaatatcttcttcggttcttatcttacaatcctttttgcagGTCTTGTACTAGTTGATTGTTCTGCAACTTATGATACTGTTGGCATGCTAAAGGATGCCGTGGATCGTGGATGTTGTGTTGTATTGGCAAACAAGAAACC

upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------gcaccaaaaaagcttacatcgtcggtgttctgtgtacaataaatttcaattgtgtttctgaatttaag-------------cccacatttcacatttcatcgtcgcattt-cagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC
                                                                      |     |||||      ||| | | | | |||| |         ||   |  | ||| | ||   |||              |     |||  || | ||  ||   ||| ||||||| || |||||||| ||||||||||||||||| |||||| || |||| || ||||| ||||||  |||||| ||||| ||||||||||||||||||||
gtctgtgatccttctccctatgcagaatacattgcgcgctaagtttttgaattctctggaatagaaaccagtggggaaaaaaaaggaatctttgatatgctgtatgattgttgattagttcctttttttaaaaaaaaggagtgtaatatcttctttggttcttatcttatgatcctttttgcagGTCTTGTACTAGTTGATTGTTCTGCAACTTATGATACTGTTGGCATGCTAAAGGATGCCGTGGATTGTGGATGTTGTGTTGTATTGGCAAACAAGAAACC
















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|211499920|gb|FL302706.1|FL302706
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGACCAACTG                         GGCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTA
EST: gi|91876333|gb|EB406290.1|EB406290
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|148966783|gb|EE017871.2|EE017871
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|32916159|gb|CF020971.1|CF020971
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTTGGAAGTACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|148952245|gb|EC898050.2|EC898050
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|211499917|gb|FL302703.1|FL302703
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTTGGAAGTACAACTG                         GTCTGGTGCTAGTTGACT
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACT
EST: gi|211066374|gb|FL302719.1|FL302719
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTTGGAAGTACAACTG                         GTCTGGTGCTAGTTG
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTG
EST: gi|101393900|gb|EB818883.1|EB818883
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTG
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTC-TGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTG
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTTGGAAGGACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|71314894|gb|DR794068.1|DR794068
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGNCA-CTTATGACACTGTTAGCCTGCTG
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTG-CAACTTATGACACTGTTAGCCTGCTG
EST: gi|71448119|gb|DR829169.1|DR829169
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|148938292|gb|EC882596.2|EC882596
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|71770930|gb|DR968867.1|DR968867
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|14191192|gb|BG833422.1|BG833422
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|93016572|gb|EB642092.1|EB642092
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAGCTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
EST: gi|94477192|gb|EB706150.1|EB706150
EST:     GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG                         GTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA
genomic: GGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 58

GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 74

GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 89

GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTGgttcgttgtt ... cgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattgtgtttctgaatttaagcccacatttcacatttcatcgtcgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC
             tgaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaccaaaaaagcttacatcgtcggtgttctgtgtacaataaatttcaattgtgtttctgaatttaagcccacatttcacatttcatcgtcgcatttcagGTCTGGTGCTAGTTGACTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - caaaaaa
- - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcccaca