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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac...

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgt-ataagtgtcagat----atcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggg------gcttgagggcccttgtac--------------------------------
||||||||||||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || || ||||||||||| | |||    | ||    || |  || | |    | |  | || |   |    |   ||  | || ||   |  ||||||||         |||| | |    ||| |                                 
GAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAGgtcacaagcaaaatatcttcataaaattttacttgaaataat-tcaaattatttgtttgcaacagctttactgttcagttgtttactaccattgcttcacgattgttggaaacctgacttgctttgtttctggcattctgtag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcagtttctgcagt-tatt-gttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac-----
||||| ||||||||||| ||||||||||| || || |||||||| || || || |||||||||||||| || ||||||||||| | ||    ||    ||||   |||| | |||  |||   | || |  | ||| | | |    |    |   |||  ||   | ||     |  |||||      
GAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAGgtgtgagctctag----cagtgaatgcaatatatcagtttgatggaaaaaattactcttcagtcat-cagtagtgttagttaccgtttctc--ctgttgtaatgggg

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G122135_T01 (Zea mays), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgt---ataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac
||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||||   || ||||    | |    | | | || ||||  |  | | || |    |   ||||   ||||   |||   | ||     |||        | | | 
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcagacttatgttt-caattat-atggtgttgatactgttg-gcattccatgtaagctgatcgtattaatacctttt---ttttggcag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGg---tataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac
||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  |||||||||   ||| ||||    | |   || | | |||  | | |  | | ||||    |  |||||   ||||   |||  |  | |     |||   |         
GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcagtgatgcaaacatgtgtttccag--aatatggtgttgacaactgttgacattccatgtaagctga--tcatctcttctttggcag---------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtata-agtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgag---ggcccttgtac---
||||| |||||||| ||||||||||| ||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| ||||||   ||  | | | | |  |     || || |   ||||    || ||||||   | |||| || ||  || |  |||||  ||  ||   ||    |   |   
GAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagcagaattaaaaaccgat----acaatt-tgcctctcatatcatgaatac-tgtcatctata-caaaaattcatttggctctatagtttggagtgtaagctca

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 7
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcag---tttctgca----gttattgttctctagacaggaatacacattatctgtatcat----gaagttgtttggggcttg------agggcccttgtac-----------------------------------------------------------------
||||| ||||| ||||||||||| |||||||| |||||| | ||||||||||||||||| ||||||||  |  | || ||||||| |     ||||| |     |||  |||    || |   |  |||       |||     ||||   | ||||     || |         ||||       | |   || |||                                                                 
GAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTAATAATGGGGATGGCTCCTATCCTTGGGAAGgtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 5'ss of exon 6
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac----
||  | |||||||| ||||||||||||||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| ||||||  || ||  |  | |||     |  ||  | ||||   |  ||  ||| ||  ||| |    | ||||   ||  |  | |     |    | || |    
GAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagtttgcaaacaga----gatgtgttggttcataatgcacaaattcattttagcatcttaatgattatgactatgtccaactgtttttcgtcctgat

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 6
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcagtttctgcagttattgttctcta--gacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac------
|||||||||| |||||| || ||||||||||| ||||| |||||||||||  |||||||||||||||| || || |||||||||  | |     ||    | || |||||||       |  |  || |||| |   || ||    | ||||    |  |    || |||| | |  ||||        
GAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAGgtaagacttcataat----ggttgtgcagttgacacagttaaaggaaaggattcatcaatagtcatttcat----tcatggaagggttgaagacaattgtcatggttg

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|151407658|gb|EV277473.1|EV277473
EST:     GGTCTGCTTTGGCTTCAGTAATGATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|17153685|gb|BM143618.1|BM143618
EST:     GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|26057519|gb|CA800433.1|CA800433
EST:     GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|254343473|gb|GR857229.1|GR857229
EST:     GCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgtcagatatcagtttctgcagttattgttctctagacaggaatacacattatctgtatcatgaagttgtttggggcttgagggcccttgtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgggg