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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttttgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG

Basic information

species Glycine max
transcript GLYMA18G47670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 4
gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttttgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG
                                                                   |   |      || || || |   || || |  ||   | |    ||| |||| |      | | | | |  ||  |   | |  ||   ||       || | |    |||  ||||| | || || || |||||||| || ||||| || ||||| || |||||||| || ||||||||||||||||
-------------------------------------------------------------------tctatgccaaattctt-tgtttttatagtctaagctgttgc----cacaattttt-----ttttgattctctatgct---gcttacatatttgcccaccctctcc---ccaacaagGTATTGTCAACTGGACTTGGCAGAATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG

upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttt-tgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG
                                                        |   |   |  ||||| | ||| |  |  |  ||| |    |      |||||||||     | |||   || | | | |||||                   | || | | |           |||| |||||||||| || ||||| ||||| |||||||| ||||| || |||||||| || ||||||||||||||||
------------------------------------------------------gtaagttgaaaattacttgtatgtatattcattgtgggaaaaatcatcgtactacagagggtattgtctaactgttgtgatttttc-------------------tgaattgagt-----------ttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG

upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttttgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG
                                                                                   |   |    | ||||  | |||||   ||||| |||| |   |    |  |  ||  | | | | || ||| | | ||||||  ||| | || |||||||||||| || || ||||||||||||||||||||||||||||| || ||||||||||| |||||||| |||||||
-----------------------------------------------------------------------------------ggttttctgtagtttcagaaactatgaagcacgatttattattaagttttcccttattctcagttttgtcaaggtcaaagttgttgttcatgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG

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|192325593|gb|FK019449.1|FK019449
EST:     CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA                         GTACTTTCTACAGG-CTTG
genomic: CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaa ... tgtcaattagGTACTTTCTACAGGGCTTG
EST: gi|213605011|gb|DB956358.1|DB956358
EST:     CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA                         GTACTTTCTAC
genomic: CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaa ... tgtcaattagGTACTTTCTAC
EST: gi|193574918|gb|FK531177.1|FK531177
EST:     TCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA                         GTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAG
genomic: TCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaa ... tgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAG
EST: gi|193437896|gb|FK403567.1|FK403567
EST:     CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA                         GTACTTTCTAC
genomic: CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaa ... tgtcaattagGTACTTTCTAC
EST: gi|254344439|gb|GR851136.1|GR851136
EST:     CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA                         GTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGA-G
genomic: CTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaa ... tgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG
            tattaat  putative branch site (score: 2)
      ttttcatattaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttttgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT