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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcatacagaaaaagaacaaaaaaacaaaaaaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt...

Basic information

species Glycine max
transcript GLYMA13G31920.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g32230.1 (Oryza sativa), 5'ss of exon 4
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaa------gctcatacagaaaaagaacaaaaaaacaaaaaaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt
|||  | || |||||  ||||||| ||||| |||||||| ||||||||||| || |||||||| ||||||||||| ||||| |||||||  || ||||||||||       ||  | |  ||  | ||  |||        | ||  | | ||    ||| ||   ||||    || ||   ||  ||  ||  ||| ||      
GGTTATTTTCTACCACTTGTTTGCAAAAGAGCTGGCACCTCACAAACCTCTTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatctacttttccctaaggaaaatgaaagccgtttcacaatttttcttactttatggaccaaata-ggttacttcttctttcttgtg--tctgaatgc---

upper sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G025242_T02 (Zea mays), 5'ss of exon 4
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat--acagaaaaagaacaaaaaaacaaaaaaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt-
|||  |||| |||||  ||||||||||||| |||||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||||  || |||||||||  |  ||   |   |   |||                 | |  | ||   |  |   |  || || |||| |   |   |   || |||||    |||| 
GGTTCTCTTCTACCACTTGTTTGCTAAAGAGCTGGCACCTCACAAGCCTCTTGCAAAGTTCTTGTGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtatacatatcatctcgacctgaatggccgtttggttccttcttcagcttttctgaaagctttatttatataactttgc--acgagtgattctct-tgatttc

upper sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G11200.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcatacagaaaaagaacaaaaaaacaaaaaaaac-ctgtgtttacatatagaatcaata-taaataattggactagctgatggttctcaaccattt
||||   || |||||||| |||||||||||  |||  || || || |||||  | || ||| ||||| ||||||| || || ||||||||||||||||||||||   | ||      ||           |     |||  |     | |||  |    |   || ||  |  ||  |  | || |  |   |  |  |   
GGTGAAATTCTACCATGTTTTTGCTAAAGAGTTGGAGCCTCATAAGCCTCTTACAAAGTTCATGTGCGTCAAAGGGATAGTGTTCTTCTGCTTTTGGCAGgtaaatacttaatttccaactttttctttgcctgccaaatgccaaaatcacaagttctctgcctactagtttcttcaatcaactaactgagtttgatgag--

upper sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
lower sequence: AT4G21570.1 (Arabidopsis thaliana), 5'ss of exon 4
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaa-gctcatacaga--aaaagaacaaaaaaacaaaaaaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt
 ||| | || ||||||||||||||||| || || || || || || || || || || ||| | ||||||||||||||||| |||||   |||||||||||||| | |   |   |  |  | | |    |||  || |   |   |||||  |||||      |||  | |  || || |  ||||   | |          
TGTGATATTCTACCATGTGTTTGCTAAGGAGCTTGCTCCTCATAATCCACTCGCAAAGTTCCTCTGCATCAAAGGAATTGTCTTCTTTGTCTTTTGGCAGgtaatgtttgcattaatcagtaaacccctcaaaacaagatttctcatgtttggatata---ctcataagattcttttgatt--ctgaaactgcag--------

upper sequence: GLYMA13G31920.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv00s0404g00020.t01 (Vitis vinifera), 5'ss of exon 4
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgta--agctcatacagaaaaagaacaaaaaaacaaaa-aaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt
 ||  | ||||| ||||||||||| || ||  ||  ||||||||| || ||  | || ||| ||||| ||||||| |||||||||||||||||||||||||||  |  ||| |           |  ||   |     ||||  |||        || | || | |  |||  |           | ||   | |  | |   
TGTCTTGTTTTATCATGTGTTTGCAAAGGAGTTGAAACCACACAAGCCCCTGACAAAGTTCATGTGCGTCAAAGGGATTGTTTTCTTCTGCTTTTGGCAGgtacaacttcacatccccttccttcttaattgctttgtaaaagttgttgaagagcattggataacttgaaagtaaaatttctatggttgaaccccttcta---

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|192303741|gb|FG996007.1|FG996007
EST:     TGGCTAAATTCTTGTGCATCAAAG-AATTGTTTTCTTCTGCTTTTGGCAG                         G-A-TGTTGCTGGA
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGA
EST: gi|192303742|gb|FG996008.1|FG996008
EST:     TGGCTAAATTCTTGTGCATCAAAGGAATTGNNNNNNNNNGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
EST: gi|298173693|gb|HO017029.1|HO017029
EST:     TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
EST: gi|9819719|gb|BE555232.1|BE555232
EST:     TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
EST: gi|208023891|gb|GD822303.1|GD822303
EST:     TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
EST: gi|8284343|gb|BE021902.1|BE021902
EST:     TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
EST: gi|9901034|gb|BE610000.1|BE610000
EST:     TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAG                         GGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT
genomic: TAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcat ... ccatgtttagGGAATGTTGCTGGAGCTTTTAGCGGCAACTGGTGTCATTCAATCTCGCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGTCTTTTACCATGTGTTTGCTAAAGAACTGGCACCACACAAACCTCTAGCTAAATTCTTGTGCATCAAAGGAATTGTTTTCTTCTGCTTTTGGCAGgtaagctcatacagaaaaagaacaaaaaaacaaaaaaaacctgtgtttacatatagaatcaatataaataattggactagctgatggttctcaaccattt

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