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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatggcgatcagaacagttcatttctcctgagttttgtgtttttttacatatatgaagtcactgaaactatggtttgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 4
---------------------gtacaa-tggc--gatcagaacagttcatttctcctgagttttgtgtttttttacatatatgaagtcactgaaactatggtttgc--gctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG
                      | ||| | ||  ||| | ||    | ||||||   |  || ||| ||| | |   |  | |  |      ||| |||| |||    | |||||||||| || |||||||| ||||| || |||||||||||||| ||||| |||||| ||||||||||||| || ||  | || |||||||  
gtatggtgtattttccttcaaattcaagtagctggattataaggaattatttctggagttttctgtatttctgtttctgaaggttgatgacaaaattatgttttttttggtgcagTATCTGCCAATTGAAGGCTTAGCTGCATTTAACAAAGCAACTGCAGAACTATTGTTTGGAGCTGATAATCCAGTACTCAAGCAAGGACGT
















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|211140316|gb|FL028761.1|FL028761
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|94477439|gb|EB706397.1|EB706397
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|71440750|gb|DR821800.1|DR821800
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211240361|gb|FL028797.1|FL028797
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|149107658|gb|EE189537.2|EE189537
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211235886|gb|FL028771.1|FL028771
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211140315|gb|FL028760.1|FL028760
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAA
EST: gi|78104308|gb|DV522726.1|DV522726
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|76289791|gb|DV029359.1|DV029359
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211140308|gb|FL028753.1|FL028753
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|148941508|gb|EC886438.2|EC886438
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211140313|gb|FL028758.1|FL028758
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTT
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTT
EST: gi|211240365|gb|FL028801.1|FL028801
EST:     GGTGAAAATCTTATGTTGGAGAAAGGAGACAACAAAGAG                         TATCTTCCCATTGAAGGGTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|78114229|gb|DV532618.1|DV532618
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211240360|gb|FL028796.1|FL028796
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211235884|gb|FL028769.1|FL028769
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|149000841|gb|EE038069.2|EE038069
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211139377|gb|FL028748.1|FL028748
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211140317|gb|FL028762.1|FL028762
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211238126|gb|FL028786.1|FL028786
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|71767561|gb|DR965498.1|DR965498
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA
EST: gi|211139376|gb|FL028747.1|FL028747
EST:     GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG                         TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAA-GCAACAGCAGAGCTA
genomic: GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTA

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: 39 (upstream exon), 48 (downstream exon)
Score: 81

GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 412

GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 65

GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 318

GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGgtacaatggc ... tgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttgtgtttttttacatatatgaagtcactgaaactatggtttgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG
         tttttttacatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatggcgatcagaacagttcatttctcctgagttttgtgtttttttacatatatgaagtcactgaaactatggtttgcgctgcagTATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT