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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC

Basic information

species Glycine max
transcript GLYMA17G10640.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
----tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgt---tgttgaaaagaaa---------attgaagttatttccatttt-ttcttgtggct---gttagTTTTTCTAGGTG------------CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC------
    | | ||| ||      ||   |   |   | | | |  | ||  || |||    || ||    |            || || | ||  | | |    | ||| |||||   |||    | | || ||             |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||      
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgttg--ttgaaaagaaaattg-aagttatttccattttttcttgtggctgttagTTTTTCTAGGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC------
          ||  ||| |    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||      
---------ctgcacctgat---tcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 1
tctcttctcttgttccttaaccatctaactcacctt---atatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagTT----TTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC---------
                | || ||     ||    ||   || | || |   |  ||||  | |||| | | | || | ||    || || | || | ||||  ||    ||| ||||   |  | |||||||| || |||||||||||| | ||||||||||| |||||| ||||||| ||||| ||||| || |||||||| || |         
---------------atcaaacagaaggctgtggtttgtatgtatcttcaatagtgtttgagagaacaatta-gtgaattggggttcttttggttggtgttgattgaaatttatagGCCGTGACTATGTCGACCCCAGCTAGGAAGAGGTTGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACA

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|16106211|gb|BI893951.1|BI893951
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|11689076|gb|BF596752.1|BF596752
EST:     TTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAG
genomic: TTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAA-CGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAG
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|4294751|gb|AI442235.1|AI442235
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|192330438|gb|FK021197.1|FK021197
EST:     AGCCATACACACATAACGG                         -TTTTCTAGGTGCTAGCAATGTCGACT-CTGCTAGGAAGAGGCTCATGAGA
genomic: AGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|298177564|gb|HO027231.1|HO027231
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCGTGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA
EST: gi|151395570|gb|EV265447.1|EV265447
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         TTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGACTCATGAGA
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... tggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC
                             tttccattttttcttg  CT-rich tract
           aaaagaaaattgaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagTTTTTCTAGGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - -gttcctt
- - - - - - - - - - ccatcta
- - - - - - - - - - - - - - ctcacct
- - - - - - - - - - - - - - - - - - - - ctccttg
- - - - - - - - - - - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa