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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtatttaaagtataactattcactgacttttgtactgatttatatgatattaactgtaacacatacttttacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCATGCGCTGTTCTAG

Basic information

species Glycine max
transcript GLYMA15G19670.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 5
----------gtgcgta--tttaaagtataactattcactga----cttttgtactgatttatatgat-attaactgtaacacata---cttttacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCATGCGCTGTTCTAG
          || |  |  |||  | ||  |  ||| |   |    || |     | |||||| |  | |||     ||    ||    |||  | ||||||||| ||||| ||  | || ||||||||||| || |||||||||||||||||||| ||||| || |
gtgcagtactgtacccagttttggactaggataatttaaaaagccactgtcaacattatttatgttctcattgctcctagtttatgtgccttacataccacagGTGTGGAATCCCATGGGCATAGTTGGTGTGATTACTGCTTTCAACTTTCCATGTGCTGTCCTTG
















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|192311334|gb|FK003791.1|FK003791
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|298176954|gb|HO026961.1|HO026961
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCA
EST: gi|254315873|gb|GR825682.1|GR825682
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|192296158|gb|FG989743.1|FG989743
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|192311335|gb|FK003792.1|FK003792
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|151412062|gb|EV281874.1|EV281874
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|15813460|gb|BI785735.1|BI785735
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|27446368|gb|CA953491.1|CA953491
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|254317668|gb|GR826652.1|GR826652
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
EST: gi|209718196|gb|BW657828.1|BW657828
EST:     ACGTCCAGATCATATGATGTTTGAG                         GTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA
genomic: ACGTCCAGATCATATGATGTTTGAGgtgcgtattt ... tacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttttgtactgatttatatgatattaactgtaacacatacttttacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCATGCGCTGTTCTAG
                                       tactttt  CT-rich tract
             atttatatgatattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtatttaaagtataactattcactgacttttgtactgatttatatgatattaactgtaacacatacttttacaccacagGTATGGAACCCACTAGGAATAGTTGGTGTAATCACTGCTTTCAACTTTCCATGCGCTGTTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT