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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA

Basic information

species Glycine max
transcript GLYMA17G00910.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattt---taattggaagggtcctttt-------cattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
               |||   ||| ||  || ||  | ||| |  | | |   | ||  |  |  ||||   | ||     |  |  ||||          |||||| || ||| |||||||||   | || | ||| ||  |||||||| ||||||| || ||||| |||||||||||||| ||||| || || |||||||| ||
---------------gttacagttcatgaggcagcct-ttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA

upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
---------gtatgttctttttttgttgttgttgatttggaagggtattc-cagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
         | || || | | | |||  ||||  | |  |    |  ||| ||| | |   |    | ||  |||   |    | |        |  |   ||||||||| ||| |||||||||   | || ||||| ||| |||||||| |||||||||||||||| |||||||||||||| ||||| || ||||||||||| ||
gtttgaatcgaat-ttatctgtctgtccttgtgtactctgctcagagttcacagaagtgaga---gattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 2
gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatga----attttaattggaagggtccttttcat-tgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
                                |   |  ||     |  |       | | || |    ||  |  |  |     || ||   || ||||||||| ||| |||||||||   | || ||| | ||| |||||||| |||||||||| ||||| |||||||||||||| ||||| || ||||||||||| ||
-nnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctgctcacaggtcgcagaagtgacagattatctgatcatgctcaggcttttctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 4
-----------------------------gtatgttc--tttttttgttgtt-gttgatttggaagggtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcatt--gcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
                             ||||  |   | |  ||| ||||  ||| |||  |    | |   ||| |||     |   | ||| |  | | |           ||   || |  |||||||| ||| | || ||||   | || ||  | ||| |||||||| |||||||||| ||||| |||||||||||||| ||||| || ||||||||||| ||
gtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtga-agtgttcaggtgtgtgtgtatca--tctgaccaattactctctgcacactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttctttt-tttgttg----ttgttgatttggaagg---------gtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
|||  |||| || | ||| |     | |  |||||    |          |||      | |   |   || | ||||| || |  ||      ||| | || ||  ||||||  ||| |||| ||||   | || ||||| ||| |||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |   |
gtagattctattatctgtgggaaactataaatttgagttgtcaattatcatatgtggacaatattatcaaagtgtatgacttgtcctttt---tgtcttcttgatc-cagCTATAATGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATA

upper sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 1
gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCA--TACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA------
             |||        |   |   |     ||| |  |||     || |  | ||||   | || |  |        ||   || ||  |    || |   ||           |   | |  ||   |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |  ||      
--------cacaattgaataaacagccataatactcccttcaaaaattgaactttcagcaaatga--ctaaactaaagatcaggattattttacaattttt-tggtgatagTTTAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAAC

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|213587273|gb|DB965935.1|DB965935
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|18730350|gb|BM525828.1|BM525828
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|9986219|gb|BE660327.1|BE660327
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|298194892|gb|HO043364.1|HO043364
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCGGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|192294916|gb|FG986639.1|FG986639
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|213613699|gb|DB963345.1|DB963345
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|19452347|gb|BM953757.1|BM953757
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
EST: gi|14259973|gb|BG882881.1|BG882881
EST:     ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCANGGATGAAAG                         CTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG
genomic: ATCTGTAATCTGCACTACTATTAACAAGGTCTGTGCATCAGGGATGAAAGgtatgttctt ... ttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA
                         ttttaat  putative branch site (score: 3)
                                        tccttttcatt  putative PPT
          acttaaatatatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctttttttgttgttgttgatttggaagggtattccagtattcccacttaaatatatgaattttaattggaagggtccttttcattgcagCTACCATGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG