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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattactctttcttcatttgtttgataatcatctatgtgtacaagtttgtaatgttcgcatctttgttttatccttttatttgtgaaaaaacattgttgctctactaatatatgcatttatctgtaagttaataatttgggtgtataaattgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAATTGGCCCTTGCAAAGTATAGACAGGTTATTTGGCAAGGGAGGGTTCTTA

Basic information

species Glycine max
transcript GLYMA09G33160.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 7
gtattactctttcttcatttgtttgataatcatctatgtgtacaagtttgtaatgttcgcatctttgttttatccttttatttgtgaaaaaacattgttgctctactaatatatgcatttatctgtaagttaataatttgggtgtataaattgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAATTGGCCCTTGCAAAGTATAGACAGGTTATTTGGCAAGGGAGGGTTCTTA
                                  ||| | |  |  | | |    |   || |||||||  | | ||| ||||  | |   | | | ||  ||||      | ||| ||  |   || ||| |||||                       |||||||||||| ||||||||||| || |||||||||||||| |||||||| ||| | || || || |||||| ||||    |||||||| || || || || |
----------------------------------tatttatgaatatctatgccttgtcca-ctttgttcaaacttttgattttaggatgtaaagtttttgtcta------tgtgctttctttaatatgttcataat-----------------------gcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
















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|151397506|gb|EV267379.1|EV267379
EST:     CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|17964389|gb|BM271125.1|BM271125
EST:     CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|21678323|gb|BQ630674.1|BQ630674
EST:     GGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: GGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|16348949|gb|BI974544.1|BI974544
EST:     CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|192308463|gb|FK000931.1|FK000931
EST:     CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|19053704|gb|BM732371.1|BM732371
EST:     AAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAG                         GATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
genomic: AAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAA
EST: gi|8282807|gb|BE020368.1|BE020368
EST:     CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTNCGATTTGATAAG                         GATATGGCAGCCCATTTCG-CCTGCGATTTTGGTGGAGGAAAAGCTGANAA
genomic: CTAGGAAAAATGCAGGGAAATTTGTTGTTCTACACCTCCGATTTGATAAGgtattactct ... tttatggcagGATATGGCAGCCCATT-CGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcatttatctgtaagttaataatttgggtgtataaattgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAATTGGCCCTTGCAAAGTATAGACAGGTTATTTGGCAAGGGAGGGTTCTTA
                  agttaat  putative branch site (score: 4)
                                         ttgtttt  putative PPT
       atttatctgtaagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattactctttcttcatttgtttgataatcatctatgtgtacaagtttgtaatgttcgcatctttgttttatccttttatttgtgaaaaaacattgttgctctactaatatatgcatttatctgtaagttaataatttgggtgtataaattgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAATTGGCCCTTGCAAAGTATAGACAGGTTATTTGGCAAGGGAGGGTTCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG