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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcacatgaactgctatcctgtatttacgaatcttgactagtctagtaatgtatgtatgtggaaatatgaaggtttctttatttctcttcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCATGCTTCCAT

Basic information

species Zea mays
transcript GRMZM2G147671_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 9
-agttcacatgaactgctatcctgtatttacgaatcttgactagtctagtaat-gtatgtatgtggaaatatgaaggtttctttatttctcttcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCATGCTTCCAT--------------------------
 | |      |||   || ||  || |    | || |  |  | | |   | | |  |  ||     |  |  ||  | | |    |  ||||| | | ||||||||||||||||||||||| ||||||||  ||||||| |||||||| | |   | |    ||    ||||| |                          
tactattttagaatcactgtca-gtttccctgcatttatatcattttctcatttgcgtacatccattatcactaaactatgtacgctcttcttcctga-cagCAAGAGAAGAAGGAAGACAAATCAGACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTTGTAAGATTTCAGTATGCTGTCTTACC

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 9
-agttcacatgaactgctatcctgtatttacgaatcttgactagtctagtaat-gtatgtatgtggaaatatgaaggtttctttatttctcttcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCATGCTTCCAT
 | |      |||   || ||  || |    | || |  |  | | |   | | |  |  ||     |  |  ||  | | |    |  ||||| | | ||||||||||||||||||||||| ||||||||  ||||||| |||||||| | |   | |    ||    ||||| |
tactattttagaatcactgtca-gtttccctgcatttatatcattttctcatttgcgtacatccattatcactaaactatgtacgctcttcttcctga-cagCAAGAGAAGAAGGAAGACAAATCAGACAAGCCAGAAGATGAGAAGAAATAAATCAACTCCTTTGTGTCTTCCTT
















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|211525285|gb|FK977008.1|FK977008
EST:     GGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: GGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|211525286|gb|FK977009.1|FK977009
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|15053742|gb|BI359287.1|BI359287
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|12968898|gb|BG265739.1|BG265739
EST:     TTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: TTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|15053743|gb|BI359288.1|BI359288
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|32937218|gb|CF042037.1|CF042037
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCGGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|28984428|gb|BQ539033.2|BQ539033
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|9733091|gb|BE511843.1|BE511843
EST:     GATCCATCTGTTAAAGATTTGCTGGCATCNATTGCACAGCNCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTG
genomic: GATCCATCTGTTAAAGATTTGCTGGCATC-ATTGCACAGC-CAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTG
EST: gi|5770174|gb|AI973348.1|AI973348
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|37382952|gb|CF628448.1|CF628448
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|15053278|gb|BI358823.1|BI358823
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|60354976|gb|DN221949.1|DN221949
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|166613681|gb|EG279092.1|EG279092
EST:     TCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: TCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
EST: gi|4609687|gb|AI600526.1|AI600526
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaatgtatgtatgtggaaatatgaaggtttctttatttctcttcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCATGCTTCCAT
                              tttctttatttctctt  CT-rich tract
                              tttctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcacatgaactgctatcctgtatttacgaatcttgactagtctagtaatgtatgtatgtggaaatatgaaggtttctttatttctcttcttaaacagCAAGAGAAGAAGGAAGACAAGTCAGACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCATGCTTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC