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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa...

Basic information

species Glycine max
transcript GLYMA19G33700.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttc-cgctcttttcccgtatcgt--tttgttcttcgccgcttgattttgttgctgcttttgttaaaccc-tagtttggtttcgcgcttaaa
|||||||||||||||||||||||| || ||  | |||||||||||||||||||| || || ||||| ||||| || ||||  ||| || | || | | |    | |   |||    | |    |    |    |||| |  |||     || |       |   | || ||     |    
GTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCGgtaagcttttcacctcgcccacaggccacaggtcgcaagtagggaatttttgaaaaatttaggggctctccctggtgcttgtgttcctaggatttattat----

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgtt-ttgttcttcgccgcttgattttgttgctgcttttgttaaac-cctagtttggtttcgcgcttaaa
|||  ||||||||||||||||||| || ||| | ||||||||||||||||||||    || || |||||||| || |||||  |  ||    |  |  ||||    | | ||| ||||||||    ||      ||  |   | ||  |     |  ||   |||  |  | |      
GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGGCACCACCGTCCATGGCACCATCACTGgtacgatg-tcttggcgaccttttttttttgttgttgttgttctttttggcggcgcgttactagggtttgcgagcggcgtctgtgttgtctatgtggcgcg-

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G027571_T02 (Zea mays), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggttt-cgcgcttaaa
||| || |||||||||||||| || || ||  | |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||  |  |   ||||      |   ||       |||      ||        ||  |    | | |||   ||   || |||   || |    
GTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggct-tcaaattttaaggtgttttgtacgatgcgt

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G027571_T01 (Zea mays), 5'ss of exon 1
-----------------------GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggttt-cgcgcttaaa
                       ||| || |||||||||||||| || || ||  | |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||  |  |   ||||      |   ||       |||      ||        ||  |    | | |||   ||   || |||   || |    
CATTTCGGTGCGCTTCGCCGCAGGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCGgtacgcttcgactctaacctctagcggggccgcgggaaaacctttaaattttctgcgatctgaagaggct-tcaaattttaaggtgttttgtacgatgcgt

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G416061_T03 (Zea mays), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa----
|||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || ||||| |||||||| |||| |    ||       || |    | ||     || |   | ||  ||    ||  ||    |   ||   ||    ||| ||  |   | | ||       
GTTCTTGATGAAGCTGAACAACGAAACGGTGACCATCGAGCTTAAGAACGGCACCGTCGTACACGGAACCATTACCGgta-tgacgtcatgcgaactttaccactgtgggaattagaggtgcggggcacctttaggtgtgcgggcttagaaag---tagcttaatactgtgtttctggctg

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctccc-----ttccgctcttttcccg---tatcgttttgt------tcttcgccgcttgattttgtt-----gctgcttttgt-----taaaccctagtttggt--ttcgcgcttaaa-------------------------------------------------------------------
|||| |||||||  ||||||||||||| || ||||||||||| |||||||| ||  ||||||| || |||||||| ||||| ||||||         | ||||| ||| |    ||  |||||||      ||| ||  ||||   | |  |     | | ||   ||      |||  ||  |   ||  || | | |||                                                                     
GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttctcttaaaaacccagctctattcgctgtttagggttttgtgtaaaatctacgatgcttacctgtaatcgatggttactcgcgtattcacaaattctgatggtgtagtttgagtttagctagtgtctttcccctaataatgctttgttggtattaaccctagtgacactggtcaagtcagatgcag

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G02840.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa--
|||| |||||||  ||||||||||||| || ||||||||||| |||||||| ||  ||||||| || |||||||| ||||| ||||||       | |   ||   |  |  |||    ||    |  | |  |    | |||||   |  || |   | ||  |  ||   | | |  
GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttctcttaaaaacccagctctattcgctgtttagggtt--ttgtgtaaaatctacgatgcttacctgtaatcgatggttactcgcgtattcacaaa

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgct-tttgttaaacc---ctagtttggtttcgcgcttaaa
|||| |||||||||| |||||||| || || ||||| |||||||||||||| || |||||||| |||||||| ||||||     ||| |||| |      |||| | ||  || ||| |||  |     | |||||||    |  |||| |   |    ||  ||||||||      |   
GTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAGgtctctctcttcctttcaa---cttccagcatt-ttctgtgcttgtctctagggttttgttcaaaccctttggtgtgcttttctcctttggtttgatatatgct

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 4
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgtttt----gttcttcgccgctt-gattttgttgctgcttttgttaaacc-ctagtttggtttcgcgcttaaa
||||||||||||| |||||||||||||||| || |||||||||||||| || || || ||||| |||||||| ||||||  | |   | |||| |   | ||  | |   ||       |||| | |    || |  |||  ||   ||   | |   |   |  |||  |||  ||      
GTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAGgt-ttttaaactcttcagtattattgtcttgatgtcgcacaagttcatgggaatttagggttttctggaactcaggcttttctgtttcttttttttttcgt-----

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ29766 (Selaginella moellendorffii), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa
 |||||||||||||| |||||||| || ||||| |||||||||||||| || ||  ||||  | || || || ||||||    ||   |  |  |||  ||||  |      |||  |||     | ||   ||| |  ||| | | ||                            
ATTTCTGATGAAGCTAAACAACGAGACAGTATCCATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgt----ttgatctctaggctagtttctagcgattgttttctctgataagtttccctttttctctggtgt-gtag--------------------------

upper sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ08912 (Selaginella moellendorffii), 5'ss of exon 2
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa
 |||||||||||||| |||||||| || ||||| |||||||||||||| || ||  ||||  | || || || ||||||    |    |  |  |||  ||||  |      |||  |||     | ||   |||    ||| | | ||                            
ATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAGgtgtgatgt--ctctaggctagtttctagcgattgttttctctgataagtttcccttttcctctggtgt-gtag--------------------------

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|208046916|gb|GD846477.1|GD846477
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|13789125|gb|BG651716.1|BG651716
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|12691282|gb|BG157618.1|BG157618
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298184695|gb|HO029908.1|HO029908
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|6913873|gb|AW395403.1|AW395403
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|58014996|gb|CX701738.1|CX701738
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|14126660|gb|BG791098.1|BG791098
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|9902628|gb|BE611526.1|BE611526
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298163152|gb|HO011885.1|HO011885
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAGACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|18848707|gb|BM567819.1|BM567819
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|19268677|gb|BM884933.1|BM884933
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|14126440|gb|BG790878.1|BG790878
EST:     CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|192311957|gb|FK004560.1|FK004560
EST:     CGTATCAATCGAGCTCAAGAACGGCGCAGTTGTTCACGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttct ... tatactgcagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAGgtactcttctcccttccgctcttttcccgtatcgttttgttcttcgccgcttgattttgttgctgcttttgttaaaccctagtttggtttcgcgcttaaa

- - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctccc