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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctatattaactttaaatctgagatatgttctgcaaatatgtatcattgacaatgttctgtctattattaactctgtag

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 5'ss of exon 12
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgta--tgctatattaactttaaatctgagatatgttctgcaaatatgtatcattgacaatgttctgtctattattaactctgtag
 ||||| |||||||||||||| |||||||| ||  | || |||||| ||||  |||||||||||||||| |||||||| ||||| ||||||||||| |  ||   |||    ||  || | | |   | ||||| |||     |  || |  |||| ||| |  | | || |||    | || ||
GTTTGACCAGGATGACTGGGAACACTATGCTAAGATGACCGCTGAAATTGGAGAGCAAGTGCAGATTGTCGGTGATGACCTCCTTGTCACCAACCCAACAgtgagtgcatagttttctattacttctaaatatgatctctctttcagtgtggttgataat-taatat-taatatatgttatgcag

upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 5'ss of exon 9
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgcta--tattaactttaaatctgagata-tgttctgcaaatatgtatcattga---caatgttctgtctattattaactctgtag
||||||||||||||||||||  |||||||| ||  | || |  ||| ||||  | ||||||||||||||||| ||||||||||| ||||||||||| |  ||||| ||  |  |||   ||   || | ||| || | |    |  |   |  |||    |||| |||   | | | || ||| || ||
ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgctaatcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaat-ttgact-tgcag

upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G048371_T01 (Zea mays), 5'ss of exon 13
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgt--atgctatattaactttaaatctgagatatgttctgcaaatat-gtatcattgaca-atgtt--ctgtctattattaactctgtag
 ||||| |||||||||||||  |||||||| ||  | || |  ||| ||||  ||||||||||||||||||||||||| || |||||||||||||| |  ||   | |  | ||   ||        ||||      |  || |   || |  ||| || | |||   | | | |||  |  | |  ||
TTTTGACCAGGATGACTGGGTTCACTATGCTAAGATGACTGAAGAAATTGGAGAGCAAGTGCAGATTGTTGGTGATGACCTTCTCGTCACCAACCCCACTgtcagtaccttgtttctttccttctaaagatgacaattaaaactccagtttggttgtcataagttacttatatcttaacattttttcag

upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G133721_T01 (Zea mays), 5'ss of exon 3
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctatattaacttta--aatctgagatatgttctgcaaatatgtatcattgacaatgt---tctgtctattattaactctgtag------------
|||||||||||||||||||      ||||| ||| | || | |||  |||| ||| ||||||||||||| || |||||||| ||||| |||||||| |  ||  |  | ||| | || |   || |           ||   || |   || | | |||  |     | | | |  | || |    ||            
ATTTGATCAGGATGACTGGAGCACTTATGCCAAACTCACTGATGAGATTGGACAGAAAGTGCAGATTGTAGGAGATGATCTTCTCGTTACCAACCCCACCgtgagtaacatttagttaactgatttcgtccccaccttgatgatgttgttcctggtcaaattaaagatatgtctggtaaagttgacagatacacaaaatc

upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G064302_T02 (Zea mays), 5'ss of exon 12
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctatattaactttaaatctgagat-atgttctgcaaatatgtatcattgacaatgttctgtctattattaactctgtag------------------
|||||||||||| ||||||      ||||| ||| | || | |||  |||| ||| ||||||||||||| || |||||||| ||||| |||||||| |  ||  |  | ||| |||    | ||||  |  |   |   |    | |      ||    ||| |     |||    || ||                     
ATTTGATCAGGACGACTGGAGCACTTATGCCAAACTCACTGATGAGATTGGACAGAAAGTGCAGATTGTAGGAGATGATCTTCTCGTTACCAACCCCACCgtgagtaacatttactagttaactgatttcgtcccccctagtcctatgcacaagatgcagttttaaacgttacctgctttggcctgtgcctgtgctgtacag

upper sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 12
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctat-attaactttaaat-ctgaga---tatgttctgcaaatatgtatcattgac----aatgt----tctgtctattattaactctgtag------------------------
||||||||||||||| |||||||||||||| ||  | ||| ||||| ||||| || |||| ||||||||||||||||||||||| || || || || |||| | ||| | | || |   |||  || | |   || | |  ||  ||    | |||   |    |||||    | ||  | ||  | ||     |                         
ATTTGATCAGGATGATTGGGAGCACTATGCAAAGATGACATCTGAAATTGGCGAGAAAGTTCAGATTGTTGGTGATGATCTCCTTGTTACAAATCCTAAGgcaagctcttactaccaccaaaagctaaaaatctaagatgagcttatgaccaccataagctcaaaatgtaagatatgcgtgtttatgacgtcaaatccctttttattgtggctgctacag

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|16996761|gb|BM086133.1|BM086133
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|58014968|gb|CX701710.1|CX701710
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|254343119|gb|GR859281.1|GR859281
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|57574275|gb|CX547250.1|CX547250
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|254320423|gb|GR826872.1|GR826872
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCT-CTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTTCTGTTGAA
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCC-TTCTGTTGAA
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|10254318|gb|BE822084.1|BE822084
EST:     NNCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|16343634|gb|BI969229.1|BI969229
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|7588392|gb|AW704189.1|AW704189
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|254329397|gb|GR838950.1|GR838950
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|58020394|gb|CX707136.1|CX707136
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|151408704|gb|EV278512.1|EV278512
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
EST: gi|254329396|gb|GR838949.1|GR838949
EST:     GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAG                         CGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG
genomic: GCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctata ... aactctgtagCGTGTGGAGAAAGCAATCAAGGAGAAGGCTTGCAATGCCCTTCTGTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgctatattaactttaaatctgagatatgttctgcaaatatgtatcattgacaatgttctgtctattattaactctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC