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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaataattctttatggctaccttgcaggtttgaatgatcgtttttgctggatatctgttcatttaacattatcttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCAGGTATTACTGTCATCCAGATTGATGAAGCTGCTCTA

Basic information

species Glycine max
transcript GLYMA13G15140.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G15140.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G20980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgaaaataattctttatggctaccttgcaggtttgaatgatcgtttttgctggatatctgttcatttaac-attatc-ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCAGGTATTACTGTCATCCAGATTGATGAAGCTGCTCTA
                     |  || |   ||  |   | | |   ||| |||| ||     | ||||| || ||| |  |||||  |||    || ||||| | ||| |||||  | || ||||| |||||||||||||| ||||| || || ||| | ||||| ||||||||||||||||||||  ||
-------------------gtgtgacatctaagcctctcaagcttcctttcgctgtatggtattccatttcaccattcttgttgtttgtagGCATGAGACATGTTTCCAAATTGCACTTGCCATCAAAGATGAGGTTGAGGACCTTGAAAAGGCTGGTGTCACTGTTATCCAGATTGATGAAGCTGCATTA

upper sequence: GLYMA13G15140.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 10
gtatgaaaataattct--ttatggctacctt-gcaggtttgaatgatcgtttttgctggatatctgttcatttaacattat--cttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCAGGTATTACTGTCATCCAGATTGATGAAGCTGCTCTA
||| |||||| |  |     |   ||| ||  |  | |||  | ||    ||||| |  | ||   |  || |||   | |  | || | |||||||||| || ||||| |||||||||||||| ||||| || ||||||||||||||||| | |||||||||||||||||||||||||||||| |||||||||
gtaagaaaatcaagccaaccaaatctatctcagtcgatttctacga----ttttgttata-atgattgaatctaatgcttttacctgatcttagATTCGAGACTTGCTATCAGATTGCTTTGGCCATCAAAGACGAGGTTGAGGATCTTGAAAGAGCAGGTATTACTGTCATCCAGATTGATGAGGCTGCTCTA
















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|57574542|gb|CX547517.1|CX547517
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|58019711|gb|CX706453.1|CX706453
EST:     GCCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCC-AG                         ATTTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagA-TTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG
EST: gi|207719852|gb|GD703037.1|GD703037
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|21257124|gb|BQ454012.1|BQ454012
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|7691802|gb|AW759923.1|AW759923
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|207811405|gb|GD783466.1|GD783466
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|6913068|gb|AW394598.1|AW394598
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|9204637|gb|BE330861.1|BE330861
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|151393115|gb|EV262990.1|EV262990
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAG-TTGAGGA
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGA
EST: gi|207836039|gb|GD807394.1|GD807394
EST:     GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAG                         ATTCGAAACTATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG
genomic: GGCCCTGTTACTATTCTGAACTGGTCCTTTGTTAGAGATGACCAGCCAAGgtatgaaaat ... ttgttattagATTCGAAAC-ATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatgatcgtttttgctggatatctgttcatttaacattatcttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCAGGTATTACTGTCATCCAGATTGATGAAGCTGCTCTA
                                atttaac  putative branch site (score: 3)
                                        ttatctt  CT-rich tract
                                atttaacattatcttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaataattctttatggctaccttgcaggtttgaatgatcgtttttgctggatatctgttcatttaacattatcttgttattagATTCGAAACATGCTACCAGATTGCTTTGGCTATCAAGGATGAGGTTGAGGATCTTGAGAAAGCAGGTATTACTGTCATCCAGATTGATGAAGCTGCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT