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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga...

Basic information

species Glycine max
transcript GLYMA06G01280.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaat-cctcacctattcttagtttggccacaaacaagctgacatgagccaaata--tttgggaacatga-
|  ||||||||||| || ||| ||||||||||  | ||||| || ||||||||||||||||| |||||       | |||    |||   |            | | | |  |||   |     | || |       ||    || ||   ||   ||| |    |  | 
AGGGTATTTTGGCGTGGTGTTCTTGAAGAGCTATTGTGGTTCATTAGTGGCTCAACAAATGCAAAGgtgcc----ttttcctttaatacatagagcaattagttgcttgatgtatgtatgagacgacctcgtttctactttgttgtgctgtattattttagtggtaaaag

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 5
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga-
|| ||||||||| | || ||||||||||| || || ||||| ||||||||||| |||| ||| |||||  |  |   |   |   |   |||   || |    |  | | | || |  | | |    ||   |  | ||   | |   |  |||   |       | 
AAGGTATTTTGGAGGGGTGTTGTTGAAGAACTCCTGTGGTTCATCAGTGGCTCGACAAGTGCAAAGgtgcttctgcttaaaatttaatatttcattggaaatgttat-atccatacgcaatctatatactgtctcgatgctttaaattacttatccagacgagccat

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G421493_T01 (Zea mays), 5'ss of exon 8
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgt----aatgatatct---tctaccaa--------------tctttttcatgcacgaa--tcctcacctat-tcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga--
|  ||||||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||||    | ||||| ||    | |||                || | ||||||  || |  |  |      | ||| |   | ||| ||  ||       || ||  |  | | | ||    ||   
AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgcagtgatagctaggccgaccggaaggtgtcgttgtgtcgtgttcatgagcgtacgtatttgttggtgtctgatggttgccgcagtcatttcctaat-agtaacttgtgttggggtttgcag

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G072608_T01 (Zea mays), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgt----aatgatatct---tctaccaat--------ctttttcatgcacgaatcctcacctattcttagtt---------tggccacaaacaa--gctgacatgagccaaatatttgggaacatga
|  ||||||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||||    | ||||| ||    | |||            | | || ||  |     |  || ||||  | | |         | ||| ||  ||    || |||  | |    | || |||       
AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgcagtgatagctaggccgaccggaaggtgtcgttgtgtcgtgttcatgagcgtacgtatttgtgggtgtctgatggttgccgcagtcatttcctaacagtaacttg-tgttggggtttgcag

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G005990_T01 (Zea mays), 5'ss of exon 5
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttggg-aacatga-
|  ||||||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||||    |   ||   |    |||  | |   |   |  |      |    ||| | | |  |    |    | | |||    ||  | |       ||||| 
AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgcaggactaaaatgggtctagtgctgtctttagccaatgatttgatttattgtaggtatttgcc--ttaatatgtattaacaactcacatgtcatgat

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga-
|  || |||||||| || ||||| ||||| || |||||||| |||||||||||||||||||| |||||    |    |  ||    |||  | |   |   |  |      |    ||  | | | |    |   | |  | | |  |   |||| |  | |   | 
AGGGTGTTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgcaggattaatatggctctagtgctatctttagccaatgttttgatttgttgtaggcttgtagctgttttccttaatctg-tattcgcaacccacat

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga-----
| |||||||||| |||| ||||||||||||||| | |||||||| ||||| ||||||||||| ||||| |||| |||||| |  |||  | |       |   |  |   || ||  |  | |     |||  |  |  |||  || |||| |   ||   ||  |     
AGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAGgttatgacatcttc-attaattgtctcagaatccatgtgttt--cttttactgttctttatgcaattacac--acacaagtcaaacagaaggagccaacactttg

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 6
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgta----atgatatc---ttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga
||||||||||||||||||||||||||||| || || ||||| |||||||||||||||||||| ||||||    ||| |||    |  ||   ||  ||| | |        | ||    ||   |    |||    |    | | ||| |||      | | | ||       
AAAGTATTTTGGCGAGGGGTTGTTGAAGAACTGCTGTGGTTCATCAGTGGCTCAACAAATGCTAAGgtatgaaatgttattgagtattatggattgtttacttcatttctccttctttcatatctttcatggtattaccagaacagacttgacttggctttctagg-------

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatc----ttctaccaatctttttcatgcac----gaatcctcacctatt----cttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga---------------------------
   ||||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||||||||||||||    ||||     || ||  |    ||||           ||        ||       || |  |||  | |         ||  |     |  | |||   |  |                              
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ36491 (Selaginella moellendorffii), 5'ss of exon 4
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga
   || |||||||| || ||||| |||||||| ||||||||||| ||||| || ||||| || ||||||  ||         |  |  |||| ||  ||| |   |||||   | |||| | |                                           
CGGGTGTTTTGGCGGGGAGTTGTCGAAGAGCTACTTTGGTTTATAAGTGGATCCACAAACGCGAAGgtagagag-----tagcgtacattttacaaacaccagatctcacagttacttactatcag----------------------------------------

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ18561 (Selaginella moellendorffii), 5'ss of exon 6
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga
   || |||||||| || ||||| |||||||| ||||||||||| ||||| || ||||| || ||||||  ||         |  |  |||| |   ||| |   |||||   | |||| | |                                           
CGGGTGTTTTGGCGGGGAGTTGTCGAAGAGCTACTTTGGTTTATAAGTGGATCCACAAACGCGAAGgtagagag-----tagcgtacattttacgaacaccagatctcacagttacttactatcag----------------------------------------

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|192311470|gb|FK005201.1|FK005201
EST:     GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG                         GTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
genomic: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatat ... gtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
EST: gi|192311469|gb|FK005200.1|FK005200
EST:     GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG                         GTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA
genomic: GGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatat ... gtatattcagGTGCTACAGGAAAAAGGCATTCATATTTGGGATGGCAATGCATCCAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatcttctaccaatctttttcatgcacgaatcctcacctattcttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga

- - - - - - - - - - - TTGAAG
- - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcacc