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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttccttaaccatctaactcaccttatatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagtttttctagGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA

Basic information

species Glycine max
transcript GLYMA17G10640.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
--------------------------------ttgttccttaacca---tctaactcaccttatatctccttgttgttg--ttgaaaagaaaattgaa-gttatttccattttttcttgtggctgttagtttttctagGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA
                                ||  ||||  |||    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| ||||   
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
ttgttccttaaccatctaactcaccttatatctccttgttgttg--ttgaaaagaaaattg-aagttatttccattttttcttgtggctgttagtttttctagGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA
 ||  ||| |    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| ||||   
ctgcacctgat---tcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 1
ttgttccttaaccatctaactcacctt---atatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagtt----tttctagGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA
       | || ||     ||    ||   || | || |   |  ||||  | |||| | | | || | ||    || || | || | ||||  ||    ||| ||||   |  | |||||||| || |||||||||||| | ||||||||||| |||||| ||||||| ||||| ||||| || |||||||| || || || || |
------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:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|48575423|gb|CO036396.1|CO036396
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGG                         GTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAG
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGgtggggtgac ... gtttttctagGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAG
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAACGGTTTTTCTAG                 
genomic: CTTGCGTTTTCCTTAAACTGCCTCATTCCGAAGCCATACACACATAAC-G--------Ggtggggtgac ... gt


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaagaaaattgaagttatttccattttttcttgtggctgttagtttttctagGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA
                                              tttttct  CT-rich tract
       aaaattgaagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttccttaaccatctaactcaccttatatctccttgttgttgttgaaaagaaaattgaagttatttccattttttcttgtggctgttagtttttctagGTGCTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA

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