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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaagagagggtgggatagtgttttattcagcaacaggtcaaagactaaaaatattatctgagaccatt...

Basic information

species Glycine max
transcript GLYMA19G29990.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: AT3G03610.1 (Arabidopsis thaliana), 5'ss of exon 6
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaa-----gcaatgcat-taactttaagaagagagggtgggatagtgttttatt-cagcaacaggtcaaagactaaaaatattatctgagaccatt
| ||||   | ||||| ||  | || || || ||  | |||||||| || || |||||||||||||| ||||||||  | |||||||||||||||||| ||||     |   |      |  |||||  |    |||     ||    |    |  |||||  || ||  ||| |||    |  ||                     
TATGGAGGCTAGCTTATCCACAGAGAGAACTACCACCTCTTAAATCTGAACTCTGGAAGGAAATGGGTTGGCAAGGAACAGACCCTTCAACAGATTTTCGgtacacaattttagctctggtcatgcaaatcttcttatatctagtcattttactgatgtttggtttcattaactggtttttg--tag--------------------

upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv14s0006g02040.t01 (Vitis vinifera), 5'ss of exon 1
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaag--agagggtgggatagtgttt-tattcagcaacaggtcaaagactaaaaatattatctgagaccatt
| ||||| || ||||| || |  |||||||| || || ||||| ||||| || |||||||| ||||| ||||||||| |||| | ||| |||||||||||||    |||  |   | ||  || ||| |   | |   | ||  |    |  ||||  | |  |  ||   |     |  |||| | ||| |           
TTTGGAACTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCATTCGACAGATTTTAGgtg---ggtagaggactatatataaacatctggtatttacagacttctcttatgttcatgtgtattaatgtgaatttggttaaacacattttag---------

upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv14s0108g00230.t01 (Vitis vinifera), 5'ss of exon 2
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaag--agagggtgggatagtgttt-tattcagcaacaggtcaaagactaaaaatattatctgagaccatt
| ||||  || ||||| || |  |||||||| || || ||||| ||||| || ||||| || ||||| ||||||||| |||| || || |||||||||||||    |||  |   | ||  || ||  |   | |   | ||  |    |  ||||  | |  |  ||   |     |   ||| | ||| |           
TCTGGAGCTTAGCTTATCCTGGTAGGGAGCTACCCTCTCTTAAGTCAGAGCTCTGGAATGAGATGGGTTGGCAAGGTACTGATCCATCGACAGATTTTAGgtg---ggtagaggactatatataaatatctggtatttacagacttctctcatgttcatgtgtattaatgtgaatttggtcaaacacattttag---------

upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv08s0056g00790.t01 (Vitis vinifera), 5'ss of exon 6
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaag--agagggtgggatagtgttt-tattcagcaacaggtcaaagactaaaaatattatctgagaccatt
| ||||  || ||||| || |  |||||||| || || ||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| |||||||||||||    |||  |   | || ||| ||| |   | |   | ||  |    |  ||||  | |  |  ||   |     |   | | | ||| |           
TCTGGAGCTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCCTTCGACAGATTTTAGgtg---ggtagaggactatacataaacatatggtatttacagacttctctcatgttcatgtgtattaatgtgaatttggtcacacacattttag---------

upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv13s0047g00160.t01 (Vitis vinifera), 5'ss of exon 1
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaagagagggtgggatagtgttttattcagcaacaggtcaaagactaaaaatattatctgagaccatt---
| ||||  || ||||| || |  |||||||| || || ||||| ||||| || |||||||| ||||| ||||||||| |||| ||||||| |||||||||||    |||  |   | ||  || ||| |   | |       |   | ||  || |  |||    || ||  |  | |   ||| |  ||  | ||  ||   
TCTGGATCTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCCTTCAATAGATTTTAGgtg---ggtagaggactatatataaacatctggta-------ttttacagacttct-ctcatgttcatgtgtattaatgtgaatttggtcaaacacattttag

upper sequence: GLYMA19G29990.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv09s0096g00560.t01 (Vitis vinifera), 5'ss of exon 1
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaag--agagggtgggatagtgttt-tattcagcaacaggtcaaagactaaaaatattatctgagaccatt
| ||||  || ||||| || | ||||||||| || || ||||| ||||| || |||||||| ||||| |||||||||  ||| |||||||||||||||| ||    |||  |   | ||  || ||| |   | |   | |   |    |  ||||  | |  |  ||   |     |   ||| | ||| |           
TTTGGAGCTTAGCTTATCCTGGCAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTATTGATCCTTCAACAGATTTTAAgtg---ggtagaggactatatataaacatctggtatttacatacttctctcatgttcatgtgtattaatgtgaatttggtcaaacacattttag---------

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|13789800|gb|BG652391.1|BG652391
EST:     CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
genomic: CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
EST: gi|6134331|gb|AW132724.1|AW132724
EST:     CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
genomic: CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
EST: gi|22523888|gb|BU082699.1|BU082699
EST:     CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
genomic: CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
EST: gi|27423797|gb|CA935317.1|CA935317
EST:     CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
genomic: CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
EST: gi|15813140|gb|BI785415.1|BI785415
EST:     CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
genomic: CTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA
EST: gi|12774852|gb|BG239718.1|BG239718
EST:     GCAAGGTTCTGACCCTTCAACAGATTTTAG                         GGGTGGAGGATTTATTTCATTA-AGAATCTCATCTTCTTTGCGATGAAGTA
genomic: GCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtc ... tggtgtgcagGGGTGGAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGAAATTGGCTTACCCGGACAGGGAGCTTCCTTCACTTAAATCAGACCTTTGGAAGGAAATGGGATGGCAAGGTTCTGACCCTTCAACAGATTTTAGgtatctggtccaaagcaatgcattaactttaagaagagagggtgggatagtgttttattcagcaacaggtcaaagactaaaaatattatctgagaccatt

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtggg