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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC

Basic information

species Glycine max
transcript GLYMA07G01570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 1
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
                                                                                  ||||  | || | |   ||||||   | | | |       || | |   |  |  |   |    ||   ||||||| | |   || ||  ||| |        ||| |    ||||||||  ||||| |||||||||||||||||||| |||||||||||||| |  |||||||| ||||| ||||| ||||||||  | ||  | || | ||| |
----------------------------------------------------------------------------------tggtagtttttgctc--tggtaaaattgaaata-tggctaagctgtacctcgctatcggtttgaaaaggctaagttaact--taccttaatgtgt-------cgatct----tcagGAAAGTGTGGAATGGGAGCACAAGAGTAAAGTGCCTGGAAAGATGCATGGGTGTGGTCACGATGCACATGTTGCTATGCTGTTGGGTTCTGCCAGGATAC

upper sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090779_T01 (Zea mays), 3'ss of exon 1
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatct-cagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
                                                                                     || ||||| | |  |  |    ||||              ||| | ||| |  |      | |||     ||   |   |||   ||   ||       ||   || | | |||||||  ||||||||||| |||||||| ||||| ||||| |||||||| | |||||| |||||||| ||||| ||||||||  | ||  | || |||||||
-----------------------------------------------------------------------------------ttttttcttgataatttaattgtagtaaa------------ctatatctgctcaaagaagtatgattatcttgtacttgtccaccagttaaaat----tgatgtcctgttttacagGAAAGTGTGGAGTGGGAACACAAGAGCAAAGTCCCTGGGAAGATGCATGGATGTGGACATGATGCACATGTTGCTATGCTGTTGGGATCTGCTAAGATTC

upper sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G51780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatctc--agGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
                                                                                                   |  |  |  | |   | || |    ||||||      | ||||| || | |   ||| |  |  |  ||| || | | ||   | ||||   ||     ||||||||||||| ||||| |||||||||||  | || || ||||||||||| || || ||||| |||||     | ||||| || || || |||||| | |
--------------------------------------------------------------------------------------------------atcatttgacttatggatcagatttcttatgtg-attttaaattacttgagttgcaagctagtggattcttatt-gaacatggtaatgatggaattgtgtagGAAATGGTGGAATGGGAACACAAGAGTAAGATTCCAGGGAAGATGCACGCTTGCGGACATGACGCTCACACTACGATGCTCCTCGGTGCTGCAAAGTTGC

upper sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G51760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
                                                                     |  | | ||  |  |  | |||||  | | ||||     || |  |     || ||| | ||||   |   |  |||           |||||             | |||   |||  |||     ||||||||||||| ||||| ||||||||||| || || || ||||||||||| ||||| ||||| |||||     | |||||||| || || |||||  | |
---------------------------------------------------------------------tgatgtgatttgcag--tttcttgaattgttggtggaattatggta-----agtgttgt-tttgttttgggtggatt----------cttattgg---------acagattatgttggattg--tgtagGAAATGGTGGAATGGGAACACAAGAGTAAGGTTCCAGGGAAGATGCACGCTTGTGGACATGACGCTCACACTACGATGCTTCTCGGTGCTGCAAAATTGC

upper sequence: GLYMA07G01570.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g02630.t01 (Vitis vinifera), 3'ss of exon 1
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaatta-attaattcctaagtttattaacacttttttgtatattccattgat-----ttgatctc---agGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
                                                                                                            || ||   ||||  ||   | | | |  ||| ||  ||| |||  |    | |     | ||||||||  |||   |||||     |||||||    |||||||||||||||||||||||||||||||| | ||||| |||||||| || ||||| || ||  | ||||| || |||||||| ||||| ||||| ||||
-----------------------------------------------------------------------------------------------------------ctatgatctcaaacaagaggtctcttcttttatttttatttatttttcccatcaaagcaaattttttgtgaattattttgatggggtttgatcttcatagGAAATGGTGGAGTGGGAGCACAAGAGTAAAATTCCTGGGAAGATGCATGCCTGTGGGCACGACTCCCATGTTGCGATGCTTCTAGGGGCTGCAAAAATTC

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|6566839|gb|AW234471.1|AW234471
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|19453062|gb|BM954472.1|BM954472
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|209704038|gb|BW673638.1|BW673638
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|254332779|gb|GR846610.1|GR846610
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|8283527|gb|BE021086.1|BE021086
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|213614854|gb|DB956976.1|DB956976
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
EST: gi|17400805|gb|BM177587.1|BM177587
EST:     AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAG                         GAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA
genomic: AGTCACCTTTTGTTGCAATAAGAACTGATATGGATGCACTTCCCATCCAGgtttcatgag ... ttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaattcctaagtttattaacacttttttgtatattccattgatttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC
         taagtttattaacact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcatgagttttatgtgtttttttttttttttcatatgcttgaaccaagattgacttttttttatgatagttttatgcgttggttctcttggttaggtggtaagggtaagacaacaaaagagttatgtttgcccttaattaattaattcctaagtttattaacacttttttgtatattccattgatttgatctcagGAAATGGTGGAGTGGGAGCACAAGAGTAAAGTACCTGGAAAGATGCACGCATGTGGTCATGATGCTCATGTCGCTATGCTTCTTGGGGCAGCAAAGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG