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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatgatcatagtcagataatctttatgtatatgcttgagagtcatattttttctcttaacattatcacaataatgtctacatattttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA

Basic information

species Glycine max
transcript GLYMA17G10640.1
intron # 3
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 3
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 3
-----tggatgatcatagtcagataatctttatgtatatgcttgagagtcatattttttctcttaacattatcacaataatgtctacatattttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA
     |   |  | || | ||  |  |  || |   | |     |  ||  | ||||   | |||||| | ||| ||| |||| |||    || |   |  ||||| ||||| ||| |||  ||||| |||||||| |||||||| ||||||||||| || || |||||||| ||||| |||||||| || ||||
tcctttttgtatttattggcattttgttcttgtacgtgtcaccaattgtactcttttacatgttaacactgtca-aattatgtttac----ttcgccatcgccagGTACGTTCAAGCTGACACTTCAGTTTACTGAAGATTATCCTAACAAGCCACCTACAGTGCGATTTGTTTCTCGGATGTTTCATCCTAACA

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110983_T04 (Zea mays), 3'ss of exon 3
--------tggatgat-catagtcagataatctttatgtatatgcttgagagtcatattttttctcttaacattatcacaataatgtctacatattttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA
        | |||  |   |    || |  ||||| ||    | ||  |  ||    || | ||  || ||  |   |   |||   ||     ||||    |   |||| ||||||||| ||| ||| || |||| ||| || ||||||||||| ||||||||||| |||||||| ||| | ||||| || || ||||
acagctcttagattctgtgtcactagcttgtctttctgagcttactacatggtttgcttctgtcctttgac--tgatatgctaactcctg----tttta---ttctcagGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA

upper sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
tggatgatcatagtcagataatctt-tatgtatatgcttgagagtcatatttt-ttctcttaacattatcacaataatgtctacata-------ttttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA
          || ||   || | |  | | ||  || | || || |||      |||| |||     ||  || | |  |||| | |       ||||||||| |  ||| |||||||| ||||  ||||| ||| | ||||| ||||||||||| |||||||| || |||||||| || || ||||| || ||||| |
---------ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA

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:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|11689076|gb|BF596752.1|BF596752
EST:     TCCTGATGATACTCCATGGGATGGAG                         GGCACGTT-AAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCA
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagG-CACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCA
EST: gi|192331367|gb|FK021035.1|FK021035
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGCTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGCTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|21888252|gb|BQ741465.1|BQ741465
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGCTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|4294751|gb|AI442235.1|AI442235
EST:     TCCTGATGATACTCCATGGGATGGAG                         GGACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|192330438|gb|FK021197.1|FK021197
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGCTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|208058951|gb|GD858983.1|GD858983
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|298177564|gb|HO027231.1|HO027231
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|254335070|gb|GR844855.1|GR844855
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
EST: gi|151395570|gb|EV265447.1|EV265447
EST:     TCCTGATGATACTCCATGGGATGGAG                         GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC
genomic: TCCTGATGATACTCCATGGGATGGAGgtgagtttgt ... agttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttttctcttaacattatcacaataatgtctacatattttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA
          tcttaac  putative branch site (score: 2)
                 attatcacaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatgatcatagtcagataatctttatgtatatgcttgagagtcatattttttctcttaacattatcacaataatgtctacatattttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA

tggatga
- - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctaca