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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag

Basic information

species Glycine max
transcript GLYMA19G13070.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g46570.1 (Oryza sativa), 5'ss of exon 5
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgt----aaccttt----ctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag
|||||| ||  ||||||| ||||| || || || || || ||||| || ||||||||||| || ||||||||  |||||||||| || || |||||||| ||| |||||       || ||      || ||   |    || |  || |  || |||  | |   |         | | |  |  ||
TGGTAGGCCTTCTGTTGCATATGATCAGCAGGGACTTGTTTTTGCCGTGGCAATGGAAGGAGGTGCTATTAAGCTATTTGATTCCCGGTCATATGACAAAgttggtattcagcttgaatctcaaaaactgtaaattcctataaggcttgcggaagttcttatcttgggtgccaaatacaat--ttcag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G168752_T01 (Zea mays), 5'ss of exon 5
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag------
|||||||||  ||||||| ||||| ||||| || || || |||||||||||||||||||| || |||||||| ||||||||||| || |||||||||||||| |||| |   ||  |    |    |     |||  || |   |  |     | |     ||       |    |  |       
TGGTAGACCTTCTGTTGCATATGATCAACAGGGACTTGTTTTTGCTGTAGCAATGGAAGGTGGTGCTATTAATTTATTTGATTCCCGATCTTATGACAAGgtatgtagtg--aatataatacagaacaaccatatatttgtggaaggtgtgtgaaatatttatcctgtgaaccaatccaatttcag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G079723_T01 (Zea mays), 5'ss of exon 5
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactg-acattgcccatattg-gtgtag------------
|||||||||  |||| || ||||| || || || || || |||||||||||||||||||| || |||||||| ||||||||||| || || ||||||||||| |||| |   ||  |    |    |      ||  || |   | | |   |    ||   | |    || ||| |  ||             
TGGTAGACCTTCTGTCGCATATGATCAGCAGGGACTTGTTTTTGCTGTAGCAATGGAAGGAGGTGCTATTAAGTTATTTGATTCCCGGTCATATGACAAGgtatgtagtg--aatgtaatacagaacagccacatatttgtggaagcctggaaggtgtgtgaaatatttatcttgtgaataaattcaatttcag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G14530.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtat-ttgtaacctttctc-tagcctttgctatg----cttttcataacttcacaacactgacattgcccatat-tggtgtag
||||||||| || ||||||||||||||||||||||| || |||||  | ||||||||||| || ||| ||||||||||||||||  | | ||||||||||||| |  | ||  ||   ||| |  ||||||    |||    || ||  ||  |  |        ||       || | |  |||||
TGGTAGACCTGCAGTTGCGTATGACCAACAAGGCCTTGTGTTTGCAATTGCAATGGAAGGAGGTGCTGTTAAATTATTTGATTCCAGGTGTTATGACAAGgttagcttcttacaatgattcacacagccttacgcatgactgctcttgttagttctaacttctaaacccaattgatctcttatgtag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0066g00720.t01 (Vitis vinifera), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag
|||| ||||  |||| || ||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| |||||||| ||||||||||||||||||| ||  |  ||   |   ||  | |||  |||  ||||  |     |   |   |  |||| |  || |||  |   
TGGTCGACCTACTGTCGCATATGACCAACAGGGCCTTGTCTTTGCGGTGGCAATGGAAGGGGGTGCTATTAAATTGTTTGATTCACGTTCTTATGACAAGgtttttacctaaaagtatcaactttcatttcatattattttgttgcaagcttgatttt--catttcaaattttgtag---

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S27_191V6.1 (Physcomitrella patens), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctt-tgct-atgcttttcataacttcacaacactgacattgcccatattggtgtag---------------------------------------------------------------------------------------------
 ||||||||||||||||||||||| ||||| ||||| || ||| ||||||| ||||||   |||||||| ||| |||||||    || ||||||||||||||| ||| || ||     | || ||  || |||| |     |||| |  ||||  |||   |  ||     | ||  |  ||                                                                                             
GGGTAGACCCGCTGTTGCGTATGATCAACAGGGCCTTGTATTTTCTGTAGCTATGGAAAATGGAGCTATCAAACTATTTGACGTACGCTCTTATGACAAGgttagtaatt-tagttaatgtccagaattatgcttacatacttcacactttcaatacat--atgttttatttgttcctagagtcccgttcgttgttctaattcttttctgcttttttggttgtaatgtgcattaagtgaagggatgtttaatagttacatgcatttcttaaacag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S109_268V6.1 (Physcomitrella patens), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaac------ctttctctagcctttgctatgcttttcataacttcacaac-actgacattgcccatattggtgtag-------------------------------------------------------------------------------------
 ||||||||||||||||||||||| || || || || || |||||||| || |||||||| |||||||||||  | |||||    || || |||||||||||| | |  |  | |       |      | |  | | |    |||   ||   |  ||   | |     ||    | || || |                                                                                       
GGGTAGACCCGCTGTTGCGTATGATCAGCAGGGTCTTGTATTTGCTGTGGCTATGGAAGGTGGAGCTATTAAGCTCTTTGACGTACGCTCCTATGACAAGgttagcaacttaatcggatggttacaatcaactctcggtcaattttgagtatggttccatttagtacttctgtttttttttgtttcattggctctcgtactgccttctcaatctgtcttgtcttgtaaacaagtgaatcgatgcttaacaaatgcatatttttctgtaacag

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ21865 (Selaginella moellendorffii), 5'ss of exon 5
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag
 || ||||   |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||  | |||||     | ||||  ||||||||  |   |  |    | ||       |||   |   |    |  | | |   |                          
GGGAAGACTGTCTGTGGCGTATGATCAACAAGGCCTGGTATTTGCTGTTGCCATGGAAGGCGGAGCAATCAAGCTGTTTGACGGAAGGTCTTTCGACAAGgtaagatgtgattgattctccaataattttatgaaagtccgaacgaatgcttcag-------------------------

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ21867 (Selaginella moellendorffii), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag
 || |||||  |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||  | |||||     | ||||  ||||||||  |   |  | |  | ||       |||   |   |    || | | |   |                          
GGGAAGACCGTCTGTGGCGTATGATCAACAAGGCCTGGTATTTGCTGTTGCCATGGAAGGCGGAGCAATCAAGCTGTTTGACGTAAGGTCTTTCGACAAGgtaagatgtgattaattctccaataattttatgaaagtccgaatgaatgcttcag-------------------------

upper sequence: GLYMA19G13070.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ06797 (Selaginella moellendorffii), 5'ss of exon 6
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag
 || |||||  |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||  | |||||     | ||||  ||||||||  | | |  |    | ||       |||   |   |    |  | | |   |                          
GGGAAGACCGTCTGTGGCGTATGATCAACAAGGCCTGGTATTTGCTGTTGCCATGGAAGGCGGAGCAATCAAGCTGTTTGACGTAAGGTCTTTCGACAAGgtaagaagtgattgattctccaataattttatgaaagtccgaacgaatgcttcag-------------------------

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|192321958|gb|FK012510.1|FK012510
EST:     CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAG                         GGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
genomic: CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtattt ... attggtgtagGGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
EST: gi|58015238|gb|CX701980.1|CX701980
EST:     CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAG                         GGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
genomic: CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtattt ... attggtgtagGGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
EST: gi|58016158|gb|CX702900.1|CX702900
EST:     CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAG                         GGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
genomic: CAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtattt ... attggtgtagGGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
EST: gi|192321957|gb|FK012509.1|FK012509
EST:     AATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAG                         GGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT
genomic: AATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtattt ... attggtgtagGGTCCCTTTGACACCTTTCTAGTTGGTGGTGACACAGCCGAAGTTTGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATTCTCGTTCTTATGACAAGgtttgtatttgtaacctttctctagcctttgctatgcttttcataacttcacaacactgacattgcccatattggtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT