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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggttagggtggaatgtgccattttaaatttggacttgggatttccaatgctatatgaatttttcttgccatctcaaacagcttgaaattaattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG

Basic information

species Glycine max
transcript GLYMA08G19640.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G102475_T03 (Zea mays), 3'ss of exon 6
taggttagggtggaatgtgccattttaaatttggacttgggatttccaatgctatatgaatttttcttgccatctcaaacagcttgaaa---ttaattc---ctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG
||  ||   || | || |  ||| |  || |||   ||     ||| |   |||    ||||  | |   ||| |||   |   |||||   || ||||    ||||||||||||| || |||||||||||||||||||||  |  |  | || ||||| || ||||| || || || | | | ||  ||
taattt---gtcgcatctaacatatgtaacttgatgttatagattcaatcacta---aaattcatttaaacatatcatggatactgaaataattgattcgttttagGCTGAGCAAAAGGTTCGTGAAGAAAGTGAAAGGCTGCGACAGCAGGAACGTGAGCAAATTGCAGAGAAGCGTAAGCGTGATATG

upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 6
-----taggttagggtgga-atgtgccattttaa-atttggacttgggatttccaatgctatatgaatttttcttgccatctcaaacagcttgaaattaattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG
     ||    ||  |    ||||| ||||| || |  | ||  |   ||||  | |   ||    | |||  ||| || ||  ||   ||    | |  ||  |||||||||||||| || |||||||||||||||| ||| ||| || ||||||||||||| ||||| ||||| || ||  ||||  ||
ggtaataaaaaagcatcttcatgtgacatttaaagaacttgatgtaatattttgagtttcatgatgaatttatttggcaact--aatgtct---gact--tttttagGCTGAGCAAAGAGCACGTGAAGAAAGTGAAAAGCTGAGGCAACAAGAGCGTGAACAAATTGCAGAAAATCGGAGACGAGATCTG
















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|208069167|gb|GD869117.1|GD869117
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|208113975|gb|GD909780.1|GD909780
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|208065323|gb|GD863057.1|GD863057
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|208176632|gb|GD979105.1|GD979105
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGG
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGG
EST: gi|207807391|gb|GD777502.1|GD777502
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|193532237|gb|FK491945.1|FK491945
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|208116357|gb|GD920380.1|GD920380
EST:     CTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: CTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|207805992|gb|GD778287.1|GD778287
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|193396761|gb|FK362333.1|FK362333
EST:     AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
EST: gi|193492048|gb|FK453464.1|FK453464
EST:     AACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA                         GCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT
genomic: AACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGAgtaagttctt ... taattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatgctatatgaatttttcttgccatctcaaacagcttgaaattaattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG
                                          aattaat  putative branch site (score: 3)
                                                ttcct  CT-rich tract
       tatatgaatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggttagggtggaatgtgccattttaaatttggacttgggatttccaatgctatatgaatttttcttgccatctcaaacagcttgaaattaattcctagGCTGAGCAAAGGGCTCGTGAAGAAAGTGAAAGGCTTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA