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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttgttactttctcattatgatttgaagatagttttgtgagaccgtattttatggcagttgtttctctgttaaaatcattcacggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGTGCATCTAGAGAGCAGATGTGGGGCTTGTTCATTGCCAAGAAAAATTGAC

Basic information

species Glycine max
transcript GLYMA05G33790.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G33790.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 3'ss of exon 11
gtgggtttgttactttctcattatgatttgaagatagttttgtgagaccgtatttta-------tggcagttg---------tttctctgttaaaatcattcacggc----tttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGTGCATCTAGAGAGCAGATGTGGGGCTTGTTCATTGCCAAGAAAAATTGAC
|||||||   ||  || |  || |  ||    |||   ||||||  | | | | ||        ||| | |||         |  ||||  |    |    |  ||     | | |||| ||||| || |||||||| |   |||||||  |||| | || |||| |  ||||  | || |||| |||||| |||||||| ||||||||||||||||
gtgggttctgtaaattttt-ttttccttctgtgatttatttgtggcatcctttctttccatcattggtaattgagttctaactccctctcatttccttggccgtggaataatcttagGAGGACTATAACGAGATTGTTGGTGGATGGAAATCAAAACTGAACAGGAGCTCATCGGGTGAACAGAGGTGGGGATTGTTCATAGCCAAGAAAAATTGAC

upper sequence: GLYMA05G33790.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 10
gtgggtttgttactttct--cattatgatttgaagat---agttttgtgagaccgtattttatggcagttgtttctctgttaaaatcattcacggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGTGCATCTAGAGAGCAGATGTGGGGCTTGTTCATTGCCAAGAAAAA-TTGAC
|||||||  ||||||       || |  ||| |   |   ||  |  |      ||  |||     | |  | | | | ||  |||   |      | |||||| |||||||| || || || |   |||||||  |||||| |   ||| |  ||    | ||||||| |||||| |||||||||||||||||||| |||| 
gtgggttctttacttctcacttttcttgtttaattgtcacagcctctttctgaagttcttttcaatattgatatttatattttaattcct------tctcagGAGGACTACAAAGATATAGTTGGTGGATGGAAATCAAAGCTGGTAAGGAGCTCAATGGGTGAGCAGAGGTGGGGATTGTTCATTGCCAAGAAAAAATTGA-
















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|23057433|gb|BU578107.1|BU578107
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|58016153|gb|CX702895.1|CX702895
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|58024450|gb|CX711191.1|CX711191
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|26058376|gb|CA801290.1|CA801290
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|192332357|gb|FK026022.1|FK026022
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|22927282|gb|BU544421.1|BU544421
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|7028740|gb|AW458523.1|AW458523
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|58023177|gb|CX709918.1|CX709918
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|10252569|gb|BE820335.1|BE820335
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
EST: gi|58021362|gb|CX708103.1|CX708103
EST:     TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAG                         GAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT
genomic: TAAATGCCCTTGAGAACAAGAAGGACGATTTTATTGGTGACTTCAGCGAGgtgggtttgt ... cggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagaccgtattttatggcagttgtttctctgttaaaatcattcacggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGTGCATCTAGAGAGCAGATGTGGGGCTTGTTCATTGCCAAGAAAAATTGAC
                                                ctttc  CT-rich tract
                                ttaaaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttgttactttctcattatgatttgaagatagttttgtgagaccgtattttatggcagttgtttctctgttaaaatcattcacggctttcagGAAGACTACAATGAGATTGTCGAAAGATGGAAGGCAAAGCAGACCAGGGGTGCATCTAGAGAGCAGATGTGGGGCTTGTTCATTGCCAAGAAAAATTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA