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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcagaaaaataacatttagaaaaaaattaaaaataaagacaacagtgccactccatgtttaccttgtcaaactgtcaaaatttatgctcatcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAAGAAATTACAAAAACTAACAAGCAAGAAGGTGCAACTCATCCTTACCAAC

Basic information

species Glycine max
transcript GLYMA10G34430.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 10
aatcagaaaaataac-atttagaaaaaaattaaaaataaagacaacagtgccactccatgtttaccttgtcaaactgtcaaaatttatgctcatctt-acagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAAGAAATTACAAAAACTAACAAGCAAGAAGGTGCAACTCATCCTTACCAAC
  |   |    |    |||||      | ||| || |    |   |       || |||    |  |    ||| | | | | | | |   ||| || ||||||| |||||||| || |  |||||||| ||||||||||| || |||||||||||| ||||||||||||||| |||||||||||| || || || ||||||
--ttgtatggctgttgatttaattctgatttagaactctgcagctccagcaagctgcatcagcatttgaggaaattctaacactgtgttagcatattcacagGCAACAATTTTTAGAGCAGGGGGAATCAGTTCTTATGATTTCCATGGTGAAGAAAATACAAAAACTAACAAACAAGAAGGTGCAGCTTATACTCACCAAC
















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|207843147|gb|GD815097.1|GD815097
EST:     TGG-CACATAACTAGGCGTAGCTTCAATTGATTCCTTCGGATTCAAAATG                         GCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
genomic: TGGTCACATAACTAGGC-TAGCTTCAATTGATTCCTTC-GATTCAAAATGgtttgcaaag ... catcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
EST: gi|308098869|gb|HO760710.1|HO760710
EST:     ACTGGTCACATAACTAGGCTAGCTTCAATTGATTCCTTCGATTCAAAATG                         GCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
genomic: ACTGGTCACATAACTAGGCTAGCTTCAATTGATTCCTTCGATTCAAAATGgtttgcaaag ... catcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
EST: gi|15813090|gb|BI785365.1|BI785365
EST:     ACTGGTCACATAACTAGGCTAGCTTCAATTGATTCCTTCGATTCAAAATG                         GCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
genomic: ACTGGTCACATAACTAGGCTAGCTTCAATTGATTCCTTCGATTCAAAATGgtttgcaaag ... catcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
EST: gi|31305430|gb|CD390633.1|CD390633
EST:     GATTCCTTCGATTCAAAATG                         GCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
genomic: GATTCCTTCGATTCAAAATGgtttgcaaag ... catcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
EST: gi|22932985|gb|BU550124.1|BU550124
EST:     GCTAGCTTCAATTGATTCCTTCGATTCAAAATG                         GCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA
genomic: GCTAGCTTCAATTGATTCCTTCGATTCAAAATGgtttgcaaag ... catcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgccactccatgtttaccttgtcaaactgtcaaaatttatgctcatcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAAGAAATTACAAAAACTAACAAGCAAGAAGGTGCAACTCATCCTTACCAAC
                                           ctcatctt  CT-rich tract
                               tcaaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcagaaaaataacatttagaaaaaaattaaaaataaagacaacagtgccactccatgtttaccttgtcaaactgtcaaaatttatgctcatcttacagGCAGCAATTTTTGGAACCTGGGGAATCTGTTCTTATGATCTCTATGGTGAAGAAATTACAAAAACTAACAAGCAAGAAGGTGCAACTCATCCTTACCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - -aaaataa
- - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - -ccactcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttatgc