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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGGATCAGAAGGTGCAACAATTCGACTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgcttataatatttaaatattaaagttgtatcaaacttgcaatcttgactgacttaaacatcactcaattacag

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 17
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 17
AACTGGATCAGAAGGTGCAACAATTCGACTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgcttataatatttaaatattaaagttgtatcaaacttgcaatcttgactgacttaaacatcactcaattacag-----------------
|||||| |||||||| ||||||||  | ||||||||||| ||||| ||||||||  | |||||||| ||  ||  |||  | || || |||| ||| || || |||| |  | |    |||| || |       |  |  |    | |||||       || |  | ||| |||||   |                 
AACTGGCTCAGAAGGAGCAACAATAAGGCTATACATTGAACAATACGAGAAGGACGCCTCAAAGATCGGCCGAGATTCTCAGGATGCTCTTGGTCCCCTGgtcagattcccagataccttaattactcccaaatttacgcataatcgatctttgtcatgtttattaacac-caattgttggtgtctgattttcacag

upper sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 18
AACTGGATCAGAAGGTGCAACAATTCGACTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgcttataatatttaaatattaaagttgtatcaa---acttgcaatcttgact---gacttaaacat-cactcaattacag
|||||| |||||||||||||| || ||  | || |||||||| |||||||||||| | ||||||| ||||||   |||  | |||||||||| ||||||||| |||    | |     ||  ||    |   | |||||     |||   ||| |  ||   | || |   || || |  ||  |||
AACTGGCTCAGAAGGTGCAACCATCCGTGTCTATATTGAGCAGTATGAGAAGGATTCGTCAAAGACTGGGAGGGATTCTCAAGAAGCCCTTGGTCCTCTTgtgagacatctctctctcttttatcaggactgtttatcaccctgcttttgatcatatcttttggctgacctatgcatttgatcccag
















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|6567274|gb|AW234885.1|AW234885
EST:     GGATCCATCATAGATTGGGAGACTTTTCAA-TGAAGCCCTTGCTCCTCTA                         GTGGAAGTTGCATTGATACTGTCGCAGATGGGAGAATTCACTGGT
genomic: GGATCCATCAAAGATTGGGAGACTTT-CAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGT
EST: gi|17519099|gb|BM188141.1|BM188141
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|254347114|gb|GR856784.1|GR856784
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|22931572|gb|BU548703.1|BU548703
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|21676542|gb|BQ628893.1|BQ628893
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|13790017|gb|BG652608.1|BG652608
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|7591524|gb|AW707255.1|AW707255
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|9899559|gb|BE608527.1|BE608527
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|8283645|gb|BE021204.1|BE021204
EST:     AGGATCCATCAAAGATTGGGAGACTTTCANATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|12772584|gb|BG237575.1|BG237575
EST:     AGGATCCATCAAAGATTGGGAGACTNTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|213608536|gb|DB974793.1|DB974793
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|10234275|gb|BE803163.1|BE803163
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|23727044|gb|BU761537.1|BU761537
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAACGAAGCACTTGCTCCTCTT                         GTGGAAGTTGCGTTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|57575048|gb|CX548023.1|CX548023
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|58017013|gb|CX703755.1|CX703755
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|15812958|gb|BI785233.1|BI785233
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|10232504|gb|BE801392.1|BE801392
EST:     AGGATCCATCAAAGATTGGGAGACTNTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATCGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|308098112|gb|HO761283.1|HO761283
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|21600532|gb|BQ610863.1|BQ610863
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGA
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGA
EST: gi|9901768|gb|BE610736.1|BE610736
EST:     AGGATCCATCAAAGATTGTGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|10256335|gb|BE824101.1|BE824101
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|193641632|gb|FK592458.1|FK592458
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
EST: gi|27423809|gb|CA935329.1|CA935329
EST:     AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTT                         GTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC
genomic: AGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgct ... tcaattacagGTGGAAGTTGCATTGAAACTTTCGAAGATGGAAGAATTCACTGGTCGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGGATCAGAAGGTGCAACAATTCGACTATACATTGAGCAATATGAGAAGGATCCATCAAAGATTGGGAGACTTTCAAATGAAGCCCTTGCTCCTCTTgtaagatgcttataatatttaaatattaaagttgtatcaaacttgcaatcttgactgacttaaacatcactcaattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC