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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGGATCAGAAGGTGCAACAATTCGATTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgcttataatatttatttaaatataaaagttctatcaaacttgcaacttgactgacttaaatatctcaattacag

Basic information

species Glycine max
transcript GLYMA08G04890.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 18
AACTGGATCAGAAGGTGCAACAATTCGATTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgcttataatatttatttaaa-------tataaaagttctatcaaacttgcaacttgactgacttaaatatctcaattacag
|||||| |||||||||||||| || ||  | || |||||||| |||||||||||| | ||||||| ||||||   |||  | ||||| |||| ||||||||| |||    | |     || | | |        ||| |   | || |  | | |     ||| ||||| ||   || |  ||  |||
AACTGGCTCAGAAGGTGCAACCATCCGTGTCTATATTGAGCAGTATGAGAAGGATTCGTCAAAGACTGGGAGGGATTCTCAAGAAGCCCTTGGTCCTCTTgtgagacatctctctctcttttatcaggactgtttatcaccctgcttttgatcatatcttttggctgacctatgcattt-gatcccag
















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|11412392|gb|BF424403.1|BF424403
EST:     CTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: CTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|22932077|gb|BU549216.1|BU549216
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|58019793|gb|CX706535.1|CX706535
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|13312083|gb|BG405734.1|BG405734
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|19269460|gb|BM885716.1|BM885716
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|6567204|gb|AW234815.1|AW234815
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|12690328|gb|BG156664.1|BG156664
EST:     AGGATCCATCAAAGATTGTGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTC
EST: gi|12691027|gb|BG157363.1|BG157363
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGA
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGA
EST: gi|193597826|gb|FK549232.1|FK549232
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|6725125|gb|AW309524.1|AW309524
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|193391580|gb|FK354155.1|FK354155
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|6071404|gb|AW100791.1|AW100791
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|14195900|gb|BE819895.2|BE819895
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|58015854|gb|CX702596.1|CX702596
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|151406289|gb|EV276104.1|EV276104
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|19453014|gb|BM954424.1|BM954424
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|57574755|gb|CX547730.1|CX547730
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|23064423|gb|BU579196.1|BU579196
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|13789290|gb|BG651881.1|BG651881
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|120530798|gb|EH258931.1|EH258931
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGGATCAGAAGGTGCAACAATTCGATTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTTgtaagatgcttataatatttatttaaatataaaagttctatcaaacttgcaacttgactgacttaaatatctcaattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC