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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtttgatataaacattcattagacatgttattggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA

Basic information

species Glycine max
transcript GLYMA05G00370.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt---attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                                                    ||  |  ||  ||  || || ||  |    ||||| |   | |||   |     || ||||||   |   ||||   |  || |  |  ||  ||    |       || ||   ||||| | ||||| ||  | |||| | | |||| |||||| |||||||| ||  |||||||||| |  || |||||||||||||| |||||||| || ||  
----------------------------------------------------gtaataattactgtcattaaaata-acctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgat--aatgtgggcttgt-----ctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

upper sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtttgatataaacattcattagacatgttattggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                                  |    | ||| || |  |    |    | | || | ||  |  | | |   |||    || |  ||   | || || | || ||||     ||||  |   |||  ||    |       |||||  |||||| | ||||| ||  | |||| | | |||| |||||| |||||||||||  |||||||||| || || |||||||||||||| |||||||| || ||  
---------------------------------gtaataattactgt-cattagaataacctaacatgatcaacc--tggtc---ttagccaaagttttg---agttaaaagcatattca-----gttttga---taatgtgggcttgt-----ctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

upper sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0587g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt--attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                                                    ||  |  ||  ||  || || ||  |    ||||| |  |   |  ||    |||| |||  ||  ||   |   |  | |  ||| |   |  | |   || |  |||||  |||||| | ||||| ||  | |||| | | |||| |||||| |||||||||||  |||||||||| || || |||||||||||||| |||||||| || |   
----------------------------------------------------gtaataattactgtcattaaaata-acctaacatgatcaacctggtcttagccaaagttt--tgagtt---aaaagcatattcagttttgataatgtgggct-tgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGGTG

upper sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 9
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt--attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                                                    ||  |  ||  ||  || || ||  | |  |||||    |   |  ||    |||| |||  ||  ||   | |    | |  ||| |   |  | |   || |  || ||  |||||| | ||||| ||  | || | | | |||| |||||| |||||||||||  |||||||||| || || |||||||||||||| |||||||| || ||  
----------------------------------------------------gtaataattactgtcattaaaata-acttaacatgaccaaactggtcttagccaaagttt--tgagttaaaacc---atattcagttttgataatgtgggct-tgtctctgtacagCCTTCCTTTTTTAGCATCAGGGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

upper sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt---attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                                                    ||  |  ||  ||  || || ||  |    ||||| |   | |||   |     || ||||||   |    |||   |  || |  |  ||  ||    |       || ||  |||||| | ||||| ||  | |||| | | |||| |||||| |||||||| ||  |||||||||| |  || |||||||||||||| |||||||| || ||  
----------------------------------------------------gtaataattactgtcattaaaata-acctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgat--aatgtgggcttgt-----ctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

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|58021049|gb|CX707791.1|CX707791
EST:     GTATTCATCTTTGTGACATAATCTCAAACCCATCATTGGGAGATGGAAAG                         CCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
genomic: GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAGgtatttggtt ... ctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
EST: gi|58017697|gb|CX704439.1|CX704439
EST:     GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAG                         CCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
genomic: GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAGgtatttggtt ... ctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
EST: gi|51341200|gb|CO982517.1|CO982517
EST:     GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAG                         CCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
genomic: GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAGgtatttggtt ... ctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
EST: gi|58014378|gb|CX701120.1|CX701120
EST:     GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAG                         CCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
genomic: GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAGgtatttggtt ... ctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
EST: gi|51344922|gb|CO985655.1|CO985655
EST:     GTATTCATCNNNNTGACATAATCTCAAACCCATCATTGGGAGATGGAAAG                         CCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG
genomic: GTATTCATCTTTCTGACATAATCTCAAACCCATCATTGGGAGATGGAAAGgtatttggtt ... ctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
                       gtctaac  putative branch site (score: 2)
                                 tctcttctgttgcttt  putative PPT
     ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtttgatataaacattcattagacatgttattggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA