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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgtttatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 5
gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgttt---atcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
                                                   ||    | ||||       ||   | |   |||  ||  || ||||| | |  |  || | | |    |  ||||| |||| || || ||||| || || || ||||||||||| ||||||||||||||||| |||||||| || || |||
------------------------------------------------gtcactttcttgacatttctttaaggaactgg-attgttgtgcaaaaattaacac-tcaatatatctcatgttctacagTCTGTTATCAAGAAGAAGTATGGGCAAGATGCTACTAATGTTGGTGATGAAGGTGGTTTTGCTCCAAACATTCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g08550.3 (Oryza sativa), 3'ss of exon 8
gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgtttatct-tacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
                                                  ||     |   |   |    ||| | || |    |     | | | |||| |  |   |   ||||||| ||||| |||| || || ||||| || || |||||||| || || ||||||||||||||||| ||||||||||| || |||
------------------------------------------------gtaattctttcatcttcattttaaaccttt-tccccatcttacgtca-ttgaaaattaattaattttatctgtacagTCTGTTATCAAGAAGAAGTATGGTCAGGATGCCACCAATGTTGGTGATGAAGGTGGTTTTGCTCCTAACATTCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 8
gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgttta-tcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
||   | |  ||||   || | |   |  |||| |   |    |    |   |   | |   |     | | ||    |||||    || | ||   | |  | |  || |||||  |||| ||| |||| ||||| || || || || || ||||| || || |||||||||||||||||||||||||| ||||| |||
gtagcattaattttattattatta--ttatttatattttgtgcattttaccccttgaaatttagtttaacatattcacattatcttagggctta---tcatgtttctatttgtttgctcttccagTCTGTAATTAAGAAAAAGTATGGTCAAGATGCAACCAATGTTGGTGATGAAGGTGGCTTTGCTCCCAATATTCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgtttatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
              |  |  |||||| |    |  || |||||  |  ||   |    |   |    ||||   |     | |    | ||   |  | ||  |    | |   |||||    |  || |||   |||||||||| || ||||| |||||||| ||||| || |||||||| ||||| ||||| ||||||||||| || |||
gtaatgggctgctatcttcattctttccatg-agttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtt----tcgttctct-gtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 8
-----gttatagttcttttcgcataac-ttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgttt--atcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
     |   || ||||||  |  |  |  ||    |||  |   | |  |   | ||| |    |       |    | ||   |   ||| |    | ||||| |    | ||| | |||  || || |||||||| ||||| || || || ||||| |||||||| |||||||||||||| ||||| || |||||||| || |||
gtaatgcagtaattctttgagtttttcactagaaatttggattgtcacgat-tagaaagatctcactttcgtgttgtattctagagatttattcaagacaaatttattgatagatctctttgcatttttcagGCTGTAATTAAGAAAAAGTATGGACAAGATGCTACAAACGTTGGTGATGAGGGTGGTTTCGCTCCTAACATTCAG

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|254320422|gb|GR826871.1|GR826871
EST:     CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
genomic: CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
EST: gi|254317870|gb|GR832038.1|GR832038
EST:     CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
genomic: CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
EST: gi|24135559|gb|BU926069.1|BU926069
EST:     CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
genomic: CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     CCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACT-ACGTNNGGTGATGA
genomic: CCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGT-TGGTGATGA
EST: gi|254343118|gb|GR859280.1|GR859280
EST:     CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
genomic: CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
EST: gi|15812359|gb|BI784634.1|BI784634
EST:     CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAG                         GCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA
genomic: CCTTCAAAGAAGCCATGAAAATGGGCGTAGAAGTATACCATCATCTAAAGgttatagttc ... tatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatcattattattagtggtcataaattgagatgttgatgtgtttatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG
                                 tgttgat  putative branch site (score: 4)
                                           tttatctt  putative PPT
      attattattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgtttatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG