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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagcgaaatagaagatgattcaagatcttagggatgtagctggctggtaagtgctagctgcagcgtctagtgcctcacatctctgtttgatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC

Basic information

species Zea mays
transcript GRMZM2G069970_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069970_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 5
---cttagcgaaatagaagatgattcaagatcttagggatgtagctggctggtaagtgctagctgca-gcgtctagtgcctcacatctctgtttgatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC
   || || | ||   || |||  | || |    | |||    |||   || | | ||  |  || | |  |||  ||  |       || ||||||||| |||||  ||||||||||||| ||||  || ||  ||||||  |||||||||||||| || |||||||||||||| ||||||||||| ||||| ||||||||||
gccctcagtggaaggcaacatgcatgaaaacaaaatggacac-gctaagtgttgattgtgaagtgaaagaatctgatgatttgtg---ctctttgatctttcagGGAAGTGCTAGGAGGCTCATAAAGGCAGCTTTGCAAGAAGCAGCCAAGAAAAGAGAAATGAGGTACTCAGATCTCAAGAAGATTGACCGTGGTGTTCGCC
















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|211105859|gb|FL435556.1|FL435556
EST:     TGATATTGTCCACAGTAGCCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: TGATATTGTTCACAGTAG-CCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211408447|gb|FL066148.1|FL066148
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|5917415|gb|AW054206.1|AW054206
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|7162239|gb|AW519846.1|AW519846
EST:     CAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: CAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211067736|gb|FL469389.1|FL469389
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211067735|gb|FL469388.1|FL469388
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|60359128|gb|DN226101.1|DN226101
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|149105828|gb|EE291424.2|EE291424
EST:     CAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: CAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211067737|gb|FL469390.1|FL469390
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|7138031|gb|AW499394.1|AW499394
EST:     TAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: TAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|78073907|gb|DV502341.1|DV502341
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211408450|gb|FL066151.1|FL066151
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|28422416|gb|CB251896.1|CB251896
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|78122490|gb|DV540874.1|DV540874
EST:     CAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: CAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|93283060|gb|EB675324.1|EB675324
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|78073908|gb|DV502342.1|DV502342
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|5268629|gb|AI770593.1|AI770593
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|60394658|gb|DN227528.1|DN227528
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|211065012|gb|FL469387.1|FL469387
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
EST: gi|148934794|gb|EC878842.2|EC878842
EST:     ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGT                         GGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA
genomic: ACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAA

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: 56

ACAACCACACGACCAGTTTCTCATATTTGCATCTGATGGACTTTGGGAGCACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

ACAACCACACGACCAGTTTCTCATATTTGCATCTGATGGACTTTGGGAGCACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

ACAACCACACGACCAGTTTCTCATATTTGCATCTGATGGACTTTGGGAGCACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

ACAACCACACGACCAGTTTCTCATATTTGCATCTGATGGACTTTGGGAGCACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagt ... gatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagcgaaatagaagatgattcaagatcttagggatgtagctggctggtaagtgctagctgcagcgtctagtgcctcacatctctgtttgatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCGCTGCAAGTGGCAGCCAAGAAAAGGGAGATGAGGTACTCAGACCTCAAGAAGATCGACCGCGGTGTTCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG