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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

Basic information

species Glycine max
transcript GLYMA01G05800.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 6
---------gtgagtgatttgagtttttctttttagtcaaattcttccaatgttt--tattgatttcaaaatgcaatttagagccaacctaa---tcgtcagctctct---attttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
         |||     |      |||| || |        ||||| |   | |   | |||| || ||||| |  |||  |    || |||      | |    |||   || | |  ||||| ||  | ||||| ||||||||||||||  | || ||||| ||||||||||||  | |||||||| |||| || |||||||||||||| 
gttagtcttgtgttccttccccactttttttatcttattggttctttctgagctcaatgttgacttaaaaat-ctttttttacatgacttaaaatctattaatgttcttcaatgtccaacagCTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG

upper sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 6
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
                       | ||    |  ||| || |  |   | ||| | |    ||  |  |||     |    || | |   ||| |   ||||||||||||  ||||||| |||||||| |||||  | || |||||||||||||| |||  | |||||||| |||| || || ||||||||||| 
------------------gtgagtgagatgtagcctttcatttgtacttggatgtta----gcggtccagatattgctctgtcctga---ctcgaccctctgcagCTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG

upper sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
                       | |   ||     |  ||   | ||||| |  |||  |  |||  |   |     |  |     | |  | |||      |||||||  || | ||||||||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| 
------------------gtaagtgaaataaccatcttgaaaaatatattgttggcaatgtataat--aacacttgtttttttaatggtttgcaattg---aaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG

upper sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
gtgag-tgatttgagtttttctttttagtcaaattcttccaatgtttt-----attgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
|| || | |||  || || |   |||  ||   |||||  | | |||       |||  || ||  || ||     | ||| |  ||| ||| | |   ||||||    ||||| || |||| || ||||||||||||||  | || ||||| |||||||||||||| ||||||||||| ||||| ||  |||| ||||| 
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaacca-caaaattgtctgattcttatttt----agCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

upper sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaa---aatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
         || | ||| ||   | |      |  ||||| |  |||    ||||      | |  | | | || ||||| | |    | | |    ||  | ||||||||||||||||||| |||||||| ||| || | || |||||||| ||||| ||||| || |||||  ||||||||||  |||| || || 
-----accctttattttatcacatgaaatgtgtatttcca-tagtttgccaattttgggtcattttattgttgaaccaacttcactaactggtt--gatgctttgcagCTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAG

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|193489011|gb|FK456708.1|FK456708
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTT
EST: gi|254321831|gb|GR837245.1|GR837245
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
EST: gi|31471470|gb|CD413498.1|CD413498
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
EST: gi|151400968|gb|EV270782.1|EV270782
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGACCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
EST: gi|15001277|gb|BI322091.1|BI322091
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
EST: gi|254340833|gb|GR854561.1|GR854561
EST:     CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCC                         CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT
genomic: CTGTCTCAGATGGTGATAATTCTGATGATGATCCATCCAGTTTTTTCTCCgtgagtgatt ... ttttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA
                         acctaat  putative branch site (score: 3)
                                      ctctctattttctgc  putative PPT
             aatttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG