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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgagacccttctgcaaatttctgacctgcaacgattggtttgcagtttctgtttctatattataatttattacttgctcaatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG

Basic information

species Glycine max
transcript GLYMA20G32030.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
caatgagacccttctgcaaatttctgacctgcaacgattggtttgcagtttctgtttctatattataatttattacttgctcaatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG
               |  | | |  ||  |   | ||  | |    ||  ||||  || |    ||| | ||   ||| |      |   |   ||  || |||| ||||| |||| |||||||||||||||||| ||| | || |||||||||||||| |||||||||||||| |||
---------------gtgagtgttagatat---atgagggctccctagaatctgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG

upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 16
caatgagacccttctg--caaatttctgacctgcaacgattggtttgcagtttctgtttctatattataa---ttta---ttacttgctcaatctaatctt-caaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG
           |||||  | |  || |  | |      | | |||| |  ||  | ||| ||  || |||   || |   | | ||   || | |  |  |   | ||||| |||| |||||||| ||| |||||||| ||||| ||| | || || ||||| ||||| ||||||||||||||||||
---------ttttctgacccatcttgtagctttttcaaaattgttttcttttcttatttttaggttttaaaagttcaaactcatttttccactttgcttgtgtgaacagGTTCGAGCTTCTGGCTTTGGGGGATGGTTCCTTCTAAGACTCTCCCTTCATGACCCTGTTCTTCCCCTTAACATTGAG

upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 16
---------------------------------caatgagacccttctgcaaatt--tctgacctgcaacgattggtttgcagtttctgtttctatattataatttattacttg-ctcaatctaatcttcaacc-----agGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG
                                   |||  |    | |||   ||   ||||| ||    ||| ||    |  |||    |   ||| |   | |  |  | || ||   | |   | |  |       || | || || ||||| ||||| ||||||||||| ||| ||||||| || ||||||||||| || ||  | ||||| |||
gtaggtgcctactactgcatctaattgatggcagcatgtcaattgtgtgcttgttggcctgacttgtttagataggcagaccatttgatatcagatactgacactagtggcctgactttttgtgtgcctggattcctaaagATTCGTGTCTCTGGGTATGGAGGATGGTTTCTGCTTCGATTATCCCTACATGATCCTGTTCTGCCGTTGAACATCGAG

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|19270601|gb|BM886857.1|BM886857
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|22931555|gb|BU548694.1|BU548694
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|6341955|gb|AW164779.1|AW164779
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|193326860|gb|FK290739.1|FK290739
EST:     CCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|58020778|gb|CX707520.1|CX707520
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|51344295|gb|CO985028.1|CO985028
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
EST: gi|208319741|gb|GE116814.1|GE116814
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGG
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGG
EST: gi|298163368|gb|HO012101.1|HO012101
EST:     CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGG                         GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT
genomic: CAATTGGCTCTGATCCAAGTCTGCACAAGGCTCCTGTGAACTATGAAGGGgtatgtttgt ... cttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttctgtttctatattataatttattacttgctcaatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG
                                      atctaat  putative branch site (score: 3)
                                            tcttc  CT-rich tract
     tctgtttctatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgagacccttctgcaaatttctgacctgcaacgattggtttgcagtttctgtttctatattataatttattacttgctcaatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG

caatgag
- - - - cccttct
- - - - - - - - - - - - - acctgca
- - - - - - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttgc