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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttatgtctgattgtcttttatagtatctatgttcgaatcctctgcgtgctcggtgacttgatattatcctgtgcttttctgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGCCCAGATAGAAGCTGAGATGAGGAAAATCGAG

Basic information

species Zea mays
transcript GRMZM2G119426_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119426_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02500.1 (Oryza sativa), 3'ss of exon 4
-----gtgcttatgtctgattgtctt-ttatagtatctatgttcgaatcctctgcgtgctcggtgacttga--tattatcctgtg-----cttttctgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGCCCAGATAGAAGCTGAGATGAGGAAAATCGAG
        || |  |||  || |||| ||  |  |   | |         | |  ||  | | | | |||    |||   | |||     || |  |||  | |||||| || ||||||||||| |||||||| || ||||| || ||||||| |||  | || |||||||| ||||| ||||| |||
gttcttcactaaactctatttctcttgttgcaaaaaaaaaggattgtctttgtatgtttttgctaaattgtcccattgatcggtgagtcactctattgcattccagATTTAAACGAGAAGAGATTAAGATCCAAGCATGGGAAGATCATCAGAGAGCAAAAATCGAAGCTGAAATGAGAAAAATTGAG

upper sequence: GRMZM2G119426_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0010g01760.t01 (Vitis vinifera), 3'ss of exon 4
--gtgcttatgtctgattgtcttttatagtatctatgttcgaatcctctgcgtgctcggtgacttgatat-tatcctgt------gcttttctgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGCCCAGATAGAAGCTGAGATGAGGAAAATCGAG
      ||   |   |     |  |  || |  ||  |  || |  | || ||     ||  ||  | || |  |||        | ||      | | ||| ||  | || |||||| |||| || || |  |||||  | |||||||||||  ||| ||||||||||||||||||||| |||
cctcaattccattatagaacttaatgaagaaattaaatg-gattattttgggtaactagtt-ctcaacatgtggcctaaaaggaggattacaaaattttcagGTTTGAACGTGAAGAGCTCAAAATACAAGTATGGGAAAATCATCAGAAAGCGAAGACAGAAGCTGAGATGAGGAAAATTGAG
















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|30088084|gb|CB886289.1|CB886289
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
EST: gi|211335942|gb|FL017252.1|FL017252
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
EST: gi|71756985|gb|DR954922.1|DR954922
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGGCCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
EST: gi|29946405|gb|CB816134.1|CB816134
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
EST: gi|148970673|gb|EE021384.2|EE021384
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
EST: gi|71440495|gb|DR821545.1|DR821545
EST:     ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAG                         ATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC
genomic: ATCCGTGCGGCTGCGTGGGAGGAGGCGGAGAAGGCCAAGTATTTAGCGAGgtgcttatgt ... tgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcctctgcgtgctcggtgacttgatattatcctgtgcttttctgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGCCCAGATAGAAGCTGAGATGAGGAAAATCGAG
                     acttgat  putative branch site (score: 5)
                                tcctgtgcttttct  putative PPT
                       ttgatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttatgtctgattgtcttttatagtatctatgttcgaatcctctgcgtgctcggtgacttgatattatcctgtgcttttctgctctgcagATTCAAGCGAGAAGAGATCAAGATCCAGGCTTGGGAGGACCATCAGAAAGCCCAGATAGAAGCTGAGATGAGGAAAATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG