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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattgtgaaatgaacatgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca...

Basic information

species Zea mays
transcript GRMZM5G899168_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G899168_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g56560.1 (Oryza sativa), 5'ss of exon 2
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaatt--------gtgaaatgaacatg-----taggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca
 ||  ||||||| |||||||| || ||||| |||||||||||||||||||| || |||||||| || | |||||||||||||||||| |  |||||||||||||||| |        ||   || | |||      | |||||   |||| | ||  |  ||| ||||  | |||| | ||||  ||||||     | | || |         
CGAGAATGGCTCGTTTGATGCTGAACTCGAAATTGGATTCAAGTTCCTTGTCGAGAGTTATGTTTCTCATGTGGAGATGGAGAAGCCAAAATATATCAAGgtgagaacttcatcatggtactatcaccatactttattggttagtacataacataccatggaacacaagcatatctagaataactaaatggt----tctgaaag---------

upper sequence: GRMZM5G899168_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G04150.2 (Glycine max), 5'ss of exon 2
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtg---agaattgtgaaatgaac---atgtag--gttatg-gcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca
|  |||||| ||||||||||| ||| | ||||||||||| || |||||||||||||||||||| || | ||| ||  |||| |  || | |  ||| |||||    |   |  |  | |  |    || |||  ||||    | |||||||||  || |  ||  |  |||  |  |  |  | |    |    |    |         
TCCAGATGGATCATTTGATGCTGAGTTGGAGATTGGATTTAAATTCCTTGTTGAAAGTTATGTTTCTCATGTTGAATTGGACAGACCAAAGCGTATAAAGgtattcaacctcctctagtatatggtatttagtagttacctacttaccttatgcttgcattcaggaggatcatggttgtgagatttttttctggttgttg---------

upper sequence: GRMZM5G899168_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G04320.1 (Glycine max), 5'ss of exon 2
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattgtgaaatga-acatg-taggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca-
|  ||| || ||||||||||| ||| | ||||||||||| || ||||| |||||||||||||| || | ||| ||  |||| || || | |  ||| |||||    |   |    ||  | ||| ||  || | |  |||||||||  || |  ||  |  |||  |  |    | |||   |    |    |||  | ||  
TCCAGACGGATCATTTGATGCTGAGTTGGAGATTGGATTTAAATTCCTCGTTGAAAGTTATGTTTCTCATGTTGAATTGGACAAACCAAAGCGTATAAAGgtattcaacctcctctggtatatggtattttgtagt-taccttatgcttgcattcaggaggatcatg-gttgtcagatgttttttgattgttgct-gttactt

upper sequence: GRMZM5G899168_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv03s0038g00650.t01 (Vitis vinifera), 5'ss of exon 2
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattgtgaaatgaaca----tgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca
|  |||||| ||||||||||| ||||| |||||||| || || || ||||||||||||||||| || | ||||||| |  | |  || | |  ||| |||||    |   ||   | |  |    |  || || |   ||          |   |  || |  |  |  ||     | || |  || |||  |   | |  |  
TCCAGATGGATCATTTGATGCGGAGCTTGAGATTGGTTTTAAATTTCTTGTTGAAAGTTATGTTTCTCATGTGGAGTTAAACAGACCAAAGACTATAAAGgtagtgaagttggttttagaagttttacagtttttctgattttcccccctttttgttaacagaaaat--taatcaaatattgtttagttttcacaattaaaa--

upper sequence: GRMZM5G899168_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv18s0001g10490.t01 (Vitis vinifera), 5'ss of exon 2
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattgtgaaatgaacatgtaggttatggca-taccttatgaatgaagacaataacatctggtataaggaa-atggcctactttcaaggctcatcaca
|  |||||| ||||||||||| ||| | |||||||| ||||| || |||||||||| |||||| |||| ||||||| |  | | ||| | ||  || ||||| |        |  |  |  |||  ||| | | | ||    |   ||   ||   |    |    | |    || |     |   || |||  |  |||  
TCCAGATGGATCATTTGATGCTGAGTTGGAGATTGGTTTCAAATTTCTTGTTGAAAATTATGTTTCCCATGTGGAGTTAAACAGGCCAAAGTGCATAAAGgtaattgactcaatttctagctgtttgttttagaagtaataaagtgatattgattttttttttctttttggttaatagaaagtcaattgaagaatgttca--

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|211341746|gb|FL188296.1|FL188296
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTA
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTA
EST: gi|37373856|gb|CF623251.1|CF623251
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|74232388|gb|DT640302.1|DT640302
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTTGGTAAACGTTTGGGA
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTT-GGTAAACGTTTGGGA
EST: gi|211064849|gb|FL464106.1|FL464106
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|74232387|gb|DT640301.1|DT640301
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|211339360|gb|FL188289.1|FL188289
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|113703127|gb|EE680631.1|EE680631
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|14244480|gb|BG842515.2|BG842515
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|88754655|gb|DY538796.1|DY538796
EST:     GGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: GGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|211244285|gb|FL461030.1|FL461030
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|40334134|gb|CK368204.1|CK368204
EST:     TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: TTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattg ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAGgtgagaattgtgaaatgaacatgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaaggctcatcaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC