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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatatttgttaaatgcagtagctgtgaataaatttctgtggtaaaaactttgtatacatgattttctttatgattgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCTCTACTTCTTGGGAGTGATTATACTGAAGGTGTAAG

Basic information

species Glycine max
transcript GLYMA01G16370.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 9
gttaatatttgttaaatgcagtagctgtgaataaatttctgtggtaaaaactttgtatacatgattttctttatgattgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCTCTACTTCTTGGGAGTGATTATACTGAAGGTGTAAG
||  ||  |  ||  ||    | | |     || |||   || |      |||   |      |||    || | || | ||||||| |||||    |||||||| ||  |  ||||| | ||||| ||||||||||| |||||||| |||||||| ||||||||||| ||
gtatatcctctttctatttcttggtt-cagttatattc--gttgc-----cttctcagcttcaattagtgttgtaat-gtttcagGACATTGAGTCTGAGCTTGGGTTATCACGAGAACAGTTAATCCGCATGGCTCTGCTTCTTGGAAGTGATTACACTGAAGGTGTTAG

upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0066g01630.t01 (Vitis vinifera), 3'ss of exon 9
-------------gttaatatttg---ttaaatgcagtagctgtgaataaatttctgtggtaaaaactttgtatacatgattttctttatgattgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCTCTACTTCTTGGGAGTGATTATACTGAAGGTGTAAG
             |||   |  |    | || |    |   ||   || |   || |   |   ||     |   ||| ||   |||| |   |  ||||||| ||||| |  ||||||||||| |  ||||||||| |||| |||||||| || ||||||||||||||||||||||| ||||| ||
ccaataaaaataagttcccaagtaaattcaagtttcttttttgattatcatgctcagcatttgcaatcgacttaccatcatccccttttttggtt-ttcagGACATTGAGACTGAGCTTGGATTAAATAGAGAAAAAGTAATTCGCATGGCACTCCTTCTTGGGAGTGATTATACTGAGGGTGTTAG
















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|193718655|gb|FK649153.1|FK649153
EST:     ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAG                         GATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
genomic: ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAGgttaatattt ... attgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
EST: gi|193693788|gb|FK628148.1|FK628148
EST:     ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAG                         GATATTGAAAAGGNGCTTGGATTGACCAGAAGAAAAATTAATACGCATGGC
genomic: ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAGgttaatattt ... attgattcagGATATTGAAAAGGAGCTTGGATTGACCAGA-GAAAAATTAATACGCATGGC
EST: gi|193514545|gb|FK471099.1|FK471099
EST:     ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAG                         GATATTGAAAAGGNGCTTGGATTGACCAGAGAAAAATTA-TACGCATGGCT
genomic: ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAGgttaatattt ... attgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
EST: gi|193699621|gb|FK640342.1|FK640342
EST:     ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAG                         GATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
genomic: ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAGgttaatattt ... attgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
EST: gi|193707851|gb|FK647647.1|FK647647
EST:     ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAG                         GATATTGAAAAGGNGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT
genomic: ACAAAAATATATTTGATGACCGCAAATATGTAGAGACATACTTCATGGAGgttaatattt ... attgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatttctgtggtaaaaactttgtatacatgattttctttatgattgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCTCTACTTCTTGGGAGTGATTATACTGAAGGTGTAAG
                                            gattgat  putative branch site (score: 4)
              taaaaactttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatatttgttaaatgcagtagctgtgaataaatttctgtggtaaaaactttgtatacatgattttctttatgattgattcagGATATTGAAAAGGAGCTTGGATTGACCAGAGAAAAATTAATACGCATGGCTCTACTTCTTGGGAGTGATTATACTGAAGGTGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG