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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttccttcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac...

Basic information

species Zea mays
transcript GRMZM5G862959_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G08050.2 (Glycine max), 5'ss of exon 7
GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACT---CAAAAgtatgtgagg--gtcaagttccttcctatctgtccttttttag--------ttccttgtatctgaacagttgatgaaattagctccaat----------aattttctccaaatattcaac----------------------------------------------------------
 | ||||||||| ||||| |||||||||||||| ||||| |||| |   |||| |||    |     | | |    ||   || | |  || | |||        |  | ||||  |||     |   |    ||  |  ||           | || | |||| || |    |                                                          
ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAGgtaacctaacctattaggaaatttgtcatgtttaattatctagagtgctcatgtcatgtacttgatttacttgaggcgctactttaaacttaaatgggaatttctttccacatgtcttccattgtcacgcatttgaatgacgtgtttactttcatttgtgttcctgctgcattcacag

upper sequence: GRMZM5G862959_T04 (Zea mays), 5'ss of exon 7
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 5'ss of exon 6
GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttccttcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac
   |||||||||||||||||||||||| ||||| |||||  |   |    || | || |   | |     |||  || ||          ||   |||        ||| ||||  || ||    | ||| ||| |||   ||| |  |  
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAG-AGgtaac--taagagctctttataact---------cagaaactttcgcaatgaca-ttgagtaacttg---ctaattattctcttgtaatctgaag-

upper sequence: GRMZM5G862959_T04 (Zea mays), 5'ss of exon 7
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttcct-tcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac
   |||||||||||||||||||||||| ||||| |||||  |       |||        ||| ||   | | |   | || |    || |   |  | |  |  | |    |  ||| |||   ||   |    |  |             
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGG-------AAGCGGTCAGAGgtaaaacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag----------

upper sequence: GRMZM5G862959_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 5'ss of exon 7
GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttccttcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac----
 | ||||||||||||||| ||||| |||||||| |||||||| | |    |  | || |   || |  |  |    ||||| | || |||||||   | |   ||         ||| || |  ||  |  ||   |  |  || | | |     
ATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAA-AGgtaataatctatataatggaaatctgacattatttagttatatattgttgccattgaagtgacatgatttcacaagatcagcaactgatgtactagattt

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|148981020|gb|EE027383.2|EE027383
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|29944943|gb|CB815388.1|CB815388
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|74236008|gb|DT643922.1|DT643922
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|13126562|gb|BG317132.1|BG317132
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|74244628|gb|DT652542.1|DT652542
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|101384361|gb|EB814225.1|EB814225
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|113703551|gb|EE681055.1|EE681055
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|50326335|gb|CO521461.1|CO521461
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAATTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|71439819|gb|DR820869.1|DR820869
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|13126563|gb|BG317133.1|BG317133
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|78084340|gb|DV512733.1|DV512733
EST:     TATGAAGTACTTGATGAAGAACCAGGTGAGGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|60345456|gb|DN212429.1|DN212429
EST:     GATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: GATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|9733040|gb|BE511792.1|BE511792
EST:     TATGAAGTACTTGACGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttccttcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac

- - - - - - -  TGAAGA
- - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - AGAGCA