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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgacaacagaatacaacaaacatacatgataggagtcaggacgtacatacagttccatttcacatttttctcttagggtcccttgttatactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 5
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 5
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 5
gcttgacaacagaatacaacaaacatacatgataggagtcaggacgtacatacagttccatttcacatttttctcttagggtcccttgttatactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG
   || | | |  ||  | || |      |  | | |||          ||        | || |   | |   || |   |  ||  |  |||| | |||||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||| ||  || ||||||||||||||||| ||||||
ctctggccatatgattaagcacagcctttttttggaagtttcttttattattgcaaaggagttgagggtctctgctgatatttactattcctactcttagGTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCTGGAGATCCAGTTTCTCGTATTGTTGGCAGTCTGAGTG

upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 3'ss of exon 5
---gcttgacaacagaatacaacaaacatacatgataggagtcaggacgtacatacagttccatttcacatttttctcttagggtcccttgttatactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG
   ||   |  |   |  ||| |     |   ||  |  | |       |   ||||  |  | || |   | |   || |   |  ||  |  |||| | ||||||||||  || ||||||| ||||||||||| || ||||||||||| |||||||| ||  || ||||||||||||||||| ||||||
gtggccatatgattaagcacagcctttttttttggca--atttcttttattattacaaatg-agttgagggtctctgctgatatttactattcctactcttagGTTGGAGCCAGTCTGCCTGTAATAGCTTCTGTGACTCGTATTATTGCCTCTGGAGATCCAGTTTCTCGTATTGTTGGCAGTCTGAGTG
















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|91876333|gb|EB406290.1|EB406290
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCCGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|148966783|gb|EE017871.2|EE017871
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|32916159|gb|CF020971.1|CF020971
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|148952245|gb|EC898050.2|EC898050
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|71448119|gb|DR829169.1|DR829169
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|148938292|gb|EC882596.2|EC882596
EST:     ATTTTCAAAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTA
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTA
EST: gi|32940949|gb|CF045768.1|CF045768
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|71770930|gb|DR968867.1|DR968867
EST:     ATTTCCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCANGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|14191192|gb|BG833422.1|BG833422
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCAT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCAT
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|93016572|gb|EB642092.1|EB642092
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT                         GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT
genomic: ATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCT

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: 47 (upstream exon), 47 (downstream exon)
Score: 66

GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 68

GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACTgtatgtttgt ... atactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacatacagttccatttcacatttttctcttagggtcccttgttatactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG
                                              tactttc  CT-rich tract
                                           ttatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgacaacagaatacaacaaacatacatgataggagtcaggacgtacatacagttccatttcacatttttctcttagggtcccttgttatactttcagGTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - caacaga
- - - - - - - - caacaaa
- - - - - - - - - - - acataca
- - - - - - - - - - - - atacatg