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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttttttggagcattttttttgtgatagatagtgaaaaaatggtagataattttggttgttattggtgactggatggtaatagtgtgttcggttggttacag

Basic information

species Glycine max
transcript GLYMA03G07420.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 5'ss of exon 4
TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttttttggagcattttttttgtgatagatagtgaaaaaatggtagataattttggttgttattggtgactggatggtaatagtgtgttcggttggttacag
|||| || || || ||  | || || ||||||||||| ||||||||||| || ||  | |||||||| ||| |||||||||  ||||||||| | || |||||||| | || ||     || |   |||   || ||| |||||||       ||| | ||     ||  |||  ||   ||||     | | |  |||||||| |||
TTGCATTTCCGACTTGCATTTCAGTAAACAACACTGTTTGTCACTTCTCACCACTGTCAAGTGATGAGACATTGTTGGAAGCAGGTGATATATTAAAGATgtaagtttcttgtgc----ttgtaactgttcaaggtagagaaaaaa-aacctgtaagtatgaaaaataaaggtc-ctttctggt-----tttttcgggttggttgcag

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 5'ss of exon 3
TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttttttggagcattttttttgtg-atagatagtgaaaaa--atggtagataattttggttgttattggt--gactggatggtaatagtgtgttc--ggttggttacag
||||||| || || ||  | ||||| ||||||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||||  | ||||||||||   | ||      |||| ||||  | || | |  |  |     |||||    ||  |||      |   ||  ||| || |  || |  || |||     ||   || ||
TTGCCTTTCCAACTTGCATTTCTGTTAACAACACTGTCTGTCATTTTTCTCCCCTTGCCAGTGACGAGACAGTGTTGGAAGATGGTGATATGTTAAAAATgtaagcactgttaaagctatttctttttagtatgggttatctatgcttatggttataaaagttgaaaccaagcagtatgacaggcttttattgatgagtttttatttaaatatag

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 3
TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagt---cttt--tttggagcattttttttgtgatagatagtgaaaaaatggtagataattttggttgttattggtgactggatggtaatagtgtgttcggttggttacag
|||| || || || || || ||||||||||||||||| ||||||||||||||| | ||  | || ||  |     | |  |     ||| |||| |||||||||||   |||   |||||| |  ||||||  | |    | ||  | | |  |||| | | ||  |   || ||     || | |  | ||  | | || ||          
TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttatttaattctggtttacaga-agtaggttacttgaggatttttt-----ctaggttctcattctatttttggaac-------

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|213616512|gb|DB965710.1|DB965710
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|14009221|gb|BG725825.1|BG725825
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|192330310|gb|FK020580.1|FK020580
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|7685524|gb|AW756172.1|AW756172
EST:     GCTCTTGCCAGTGATGATACAGTGTTGGAAGATGGCGATATAGTGTAAAT                         TGACATGGCTAGCCATATAGATGGGTTCATTGCTGCTGTGCCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|151393031|gb|EV262906.1|EV262906
EST:     AGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTCCATTGCTGCTGTGGCACACACTCA
genomic: AGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|151408709|gb|EV278517.1|EV278517
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGAGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|213591699|gb|DB969799.1|DB969799
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|192299906|gb|FG991780.1|FG991780
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
EST: gi|18726869|gb|BM523802.1|BM523802
EST:     CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAAT                         TGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA
genomic: CCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttt ... ttggttacagTGACATGGCTTGCCATATAGATGGGTTCATTGCTGCTGTGGCACACACTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagtcttttttggagcattttttttgtgatagatagtgaaaaaatggtagataattttggttgttattggtgactggatggtaatagtgtgttcggttggttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG