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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctttattttattggacaatgtttattgttgtgaatgccacatgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG

Basic information

species Glycine max
transcript GLYMA17G34020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 4
gtatgctctttattttattggacaatgtttattgttgtgaatgc-cacatgttttcttgt---gcttactttgttgaa-------atacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG
||| | | |  | |  ||||     || ||    || |   |   || || |  ||| |     |  ||| || |  |       || ||||||||||||| |||||||| || ||||||||||||||| | |||   || ||||| || |  ||      | | |||  | ||||||| ||||| ||||| |
gtaagttgtgcactcaattgatgcttgcttgaccttctatttattcatatatgctctggattaacaaactgtgatatataaatgtattcacagAGCAAGGAAGAGAAGTACTTCATTCACAACCATTTGTCATTTTTAGTGAAGTACCACAAGGACGATGATTCAGAACTTTCTAGAATAGTGGGATTTGAGG

upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgctctttattttattggacaatgtttattgttgtgaatgcca-catgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG
||| |     |  |  |||   || | |||   ||||    ||  | |||| |||  |   |   | || ||   ||  ||||||||| ||| | ||||||||||| ||||| || ||||| || ||||||  ||||||||||||||  |  || ||  |||| || |||||||| ||||| |
gtaagtaggct--tggattcttcactatttgc-gttgcatgtgatagcatgattttctaaac---cgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG

upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 4
gtatgctcttta--ttttattggacaatgttta-ttgttgtgaatgccacatg-ttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG
||| |    |||  | ||| |        | || ||||||  | ||   |||| ||||| | |||||||||| |    ||| ||||| |||||| |||||||||||||| ||||| ||||||   ||||| ||||||| ||||| ||||   |  ||||| || || || |||||||| ||||| |
gtaagtagattagctattagtaacaggaatctagttgttgccattgt-gcatgcttttcatttgcttactttataattatatacagAACAAGGAAGAGAAGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGG

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|213620512|gb|DB959212.1|DB959212
EST:     CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGG                         AGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAG
genomic: CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGGgtatgctctt ... aaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAG
EST: gi|213598705|gb|DB964271.1|DB964271
EST:     CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGG                         AGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGG
genomic: CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGGgtatgctctt ... aaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGG
EST: gi|213599111|gb|DB962218.1|DB962218
EST:     CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGG                         AGCAAGGGAG-AGAAGTATTTTATTCACAACCATTTGGCTTTTACT
genomic: CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGGgtatgctctt ... aaatacacagAGCAAGG-AGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACT
EST: gi|209718610|gb|BW674736.1|BW674736
EST:     CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGNG                         AGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAG
genomic: CTGTTTATCAACTCGGTTTCCATGTTGGACTCAAAGGGCTGTATAGTGGGgtatgctctt ... aaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgttgtgaatgccacatgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG
                               tgcttac  putative branch site (score: 2)
                                          ttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctttattttattggacaatgtttattgttgtgaatgccacatgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG