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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctatgcacatattaatgacattttatatcagtctggttctaccatcctgtattatacaatgtattgactgaaatatgcttttgaaaaaaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCC

Basic information

species Zea mays
transcript GRMZM2G495626_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G495626_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g67160.1 (Oryza sativa), 3'ss of exon 5
--ttgctatgcacatattaatgacattttatat-cagtctggt--tctac-catcctgtattatacaatg---tattgactgaaatatgcttttgaaaaaaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCC
   |  | ||      ||     ||   | ||| |  | ||||  | ||  ||    ||||||| || |     ||||||| |||    ||| | || |    ||||| ||||||| ||||||||||| |||||||||||||| | |||||| |||||||||||||||||||||||||||||||| |||  ||| | ||||        
gtatagtgtgtgatagtttgcctcagcctgtataccttatggtaatttattcagggagtattatgcattaagccattgactaaaaccgacttcttaata----gGTTGTTGGGAACTCCTACTGAGGAGCAGTGGCCTGGAGTAACTGATTTGAGGGACTGGCATGAGTTTCCACAGTGGAAGCCACAGATTTTAGAACGTCAA-----

upper sequence: GRMZM2G495626_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0056g00210.t01 (Vitis vinifera), 3'ss of exon 3
-----ttgctatgca-catattaatgacattttatatcagtctggttctaccatcctgtattatacaatgtattgactgaaatatgcttttgaaaaaaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCC
      |  | || | | ||||  ||  | || || ||    ||   ||   ||  | |        |    || | |   || | || |     |||||||||| ||||||| || |||||| |||||||||||||||| |||  | | || ||||||||||  | |||||||||| | || ||    ||||||||||       
tgtatctattttgtatcctattcctg-taattcatgtccaaatgccactgtgattttcttcctcttgactctttcatttttattttctatcttggaaaaagGTTGTTGGGAACGCCAACTGAGAAACAGTGGCCTGGAGTTAGTTCTCTGAGAGACTGGCATGTCTATCCACAGTGGGAACCTCAAAACTTGGCACGTGCT-----
















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|71431608|gb|DR812658.1|DR812658
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGATTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|213167909|gb|FM191321.1|FM191321
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|30306650|gb|CD001323.1|CD001323
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|71450236|gb|DR831286.1|DR831286
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|88755349|gb|DY539490.1|DY539490
EST:     TTTCTTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|87155782|gb|DY400571.1|DY400571
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|76294289|gb|DV033857.1|DV033857
EST:     TTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTTAGGTTGGCT                         -GGGAACACCTACTGAAGAACAGTGGGCCTGGAGT
genomic: TTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC--CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGG-CCTGGAGT
EST: gi|50328765|gb|CO523891.1|CO523891
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|5005601|gb|AI711663.1|AI711663
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|74238746|gb|DT646660.1|DT646660
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGAAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|211362664|gb|FL128442.1|FL128442
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACA
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACA
EST: gi|29947506|gb|CB816691.1|CB816691
EST:     TTTCCTGG-GACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAG-GGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|18178648|gb|BM379858.1|BM379858
EST:     AGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: AGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|31558281|gb|CD527493.1|CD527493
EST:     GACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAG-GGCCTGGAGTGAGTGATTTAAGGGAC
genomic: GACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|110195341|gb|EC877238.1|EC877238
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|76289583|gb|DV029151.1|DV029151
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGG
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGG
EST: gi|50336412|gb|CO531538.1|CO531538
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|9254753|gb|BE345221.1|BE345221
EST:     CCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: CCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|60343112|gb|DN210085.1|DN210085
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|5081226|gb|AI738383.1|AI738383
EST:     TGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|78027249|gb|DV495636.1|DV495636
EST:     GGTGACTTGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: GGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|76908586|gb|DV163013.1|DV163013
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|211301653|gb|FL434049.1|FL434049
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|91878647|gb|EB408604.1|EB408604
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|149110995|gb|EE294494.2|EE294494
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|29577107|gb|CB617219.1|CB617219
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|71313275|gb|DR793171.1|DR793171
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGCT                         -GGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTC-CTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|31558280|gb|CD527492.1|CD527492
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|4967165|gb|AI691873.1|AI691873
EST:     TTTCCTGGT-ACTCGGAGTTGCAACAGTTGCTTCA-ATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|22935988|gb|BU572263.1|BU572263
EST:     TTTCCTGG-GACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
EST: gi|91873993|gb|EB403950.1|EB403950
EST:     TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTTGC-                         TGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC
genomic: TTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGG-TCCTtttctttcct ... aaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcctgtattatacaatgtattgactgaaatatgcttttgaaaaaaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCC
                   tattgac  putative branch site (score: 2)
                            aaatatgcttttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctatgcacatattaatgacattttatatcagtctggttctaccatcctgtattatacaatgtattgactgaaatatgcttttgaaaaaaaaggttgcTGGGAACACCTACTGAGGAACAGTGGCCTGGAGTGAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - tatgcac
- - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - -ctggttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctt