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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA

Basic information

species Glycine max
transcript GLYMA17G04720.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 3
gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
||  | |    |   | | |||| |  |  | |  ||  ||  | | |   | || ||  ||||  |     | ||||||      ||||||| |||| |||||||| ||||| || || || ||||| ||||| |||||||| |||||||||||||| ||| |||| ||||| || || ||||| || |
gtctgcacccgtcaattttcctacgcataacctc-atcacaaatatctgacgattttatttaacacaactgctaattcttcact--acagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCCATTGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTTTACCAGAAGGCCA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 2
gttag-aatggcttgttatccctatgtgtctc---ttttataccatgttt--atcctgtttctagctaacttattacat-tattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA----------------------------------------------------------------
||| | | |    |||| |  ||   || ||    |  |  | |||   |  | | | ||    | |  || |  |    || || | ||  |||||||| |||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||||||||| ||| |||| ||||| ||||| ||||| || |                                                                
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagaggctggtttatggggccaaggcagaggctgccatcgccattggatttgatgacttcattgcagATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCAACTTGGAGATCAAGAAAGCTGACGGCAATGGTGCATTGATCGCTGAGCAAGTCTTTGAAAAGAC

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
gttag-aatggcttgttatccctatgtgtctc---ttttataccatgttt--atcctgtttctagctaacttattacat-tattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
||| | | |    |||| |  ||   || ||    |  |  | |||   |  | | | ||    | |  || |  |    || || | ||  |||||||| |||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||||||||| ||| |||| ||||| ||||| ||||| || |
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
gttagaatggcttgttatccctatgtgtc-tcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
|||   ||  |||    | | |||   || | |  || |  || |  | | |||| ||        | ||     || || |      |||||| |||| |||||||| ||||| || || |||||||| ||||| ||||||||||||||||| ||||| ||  |||| ||||| | ||||||||| || |
gttg--atttcttaacttacatattcttcatatgatagaatatatggagcatgttactgatagcaatcttgttcaatgctgtact--gcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 4
-gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaa--cagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
  | | |||    |||| |   |   |       |     ||    ||  |  |     | |  || |      ||    |  |  ||  |||||| |||||||||| || ||||| ||||| || || || ||||||||||| || |||||||||||||| ||| |||| ||||| ||||| ||||| || |
gttcataatttactgttttgattgcctaaacagatataggcacagctagacattactgcgttgtctaacattcctacatgtcctgcaatgcagAGGCTGGTTTATGGGGCCAAGGCGGAGGCTGCCATCGCCATTGGGTTTGACGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G050405_T01 (Zea mays), 3'ss of exon 3
gttagaatggc-ttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaa--cagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
|||   |   |  |||| |   |   |       |     ||  |  |   | |       |  || | |    ||    | ||  ||  |||||| |||||||||| || ||||  ||| | || ||||| ||||| || ||||| |||||||||||||| ||| |||| | ||| ||||| ||||| |  |
gttcataccccactgttttggttgcctaaactcataggcacaactagaaattatcgaatcatgtctaactttcctacctgtcttgcaatgcagAGGCTGGTTTATGGGGCCAAGGTAGAGTCTGCCATTGCCATTGGATTCGATGACTTCATTGCAGATGCTCTGAGAGGCATTGGGTTCTACCAGAAGGATA

upper sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaa-cagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
  ||  ||| |     |   |||                  |  | ||    ||| |  | |        |||   |||  || ||| |||||||||||||||||||| || || || ||||| || || || ||||||||||| ||||| || |||||  || |||| || ||  | || |||||| | |
-gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

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|298176038|gb|HO015443.1|HO015443
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|192328192|gb|FK020439.1|FK020439
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|16347143|gb|BI972738.1|BI972738
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|16347848|gb|BI973443.1|BI973443
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|5752974|gb|AI960261.1|AI960261
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|6964020|gb|AW432713.1|AW432713
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAACGCTGATGCAGCAATTGCTATCGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|14126393|gb|BG790831.1|BG790831
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|21888734|gb|BQ741947.1|BQ741947
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|209723270|gb|BW651277.1|BW651277
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTCGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGA
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTT-GGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGA
EST: gi|209723271|gb|BW651278.1|BW651278
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|151400238|gb|EV270052.1|EV270052
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|14990698|gb|BI316371.1|BI316371
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAAGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|151407408|gb|EV277223.1|EV277223
EST:     GTTAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|120532313|gb|EH260446.1|EH260446
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|21888733|gb|BQ741946.1|BQ741946
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAG                         AGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT
EST: gi|14990622|gb|BI316295.1|BI316295
EST:     GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAT                         AGGTTGGTTTATGGAGCGAAAGCTGANGCAGCAATTGCTATTGGGTTTGAT
genomic: GTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAATTAAGgttagaatgg ... tttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatgtttatcctgtttctagctaacttattacattattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
                      agctaac  putative branch site (score: 2)
                                   cattattctttttct  putative PPT
                         taacttattacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA