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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctattgctggctgtatggaaaaggctgatattcttatgcctgtaaatttgtaatgtcacctaacaaaaatgacatagcttaagtgagatattcta...

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 11
splice site 5'
intron type U2

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|6020771|gb|AW065579.1|AW065579
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5871671|gb|AW018142.1|AW018142
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATCCAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5361143|gb|AI795758.1|AI795758
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|211038831|gb|FL468651.1|FL468651
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32919709|gb|CF024521.1|CF024521
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|40302745|gb|CK347132.1|CK347132
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA

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: 40 (upstream exon), 49 (downstream exon)
Score: 11

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 9

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 10

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctattgctggctgtatggaaaaggctgatattcttatgcctgtaaatttgtaatgtcacctaacaaaaatgacatagcttaagtgagatattcta

- - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - AAGAAC