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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgcttcatatcttcaccttaaaaccaggtcaacaatccaaaggatgaaatgtttagtttgggcatgtgattttacatttgtttatttttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACCGTATGCTGAAGCAGTTTGTAGTAGCAGAACCTGAGATCCAG

Basic information

species Glycine max
transcript GLYMA14G31890.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------------------------acatgcttcatatcttcaccttaaaaccaggtcaacaatccaaa-----ggatgaaatgtttagtttgggcatgtgattttac----atttgtttatttttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACCGTATGCTGAAGCAGTTTGTAGTAGCAGAACCTGAGATCCAG
                                                                       |||   || |  ||     ||      | ||||   |   | |     ||| || |  |  |  ||| |  | | || || |      | ||  ||     |   |||| ||||||||||| || || || || ||||||||||| || ||||| |||||  || ||||||| ||||| || ||||| |||||||| |||
gtaagtcctgcttccatcaacacctagagtaccacacaatactacaatatctgtgttctaatctgagttgccatagatcgtgcctgtttattttggagaagtcactgacatacataggtggaggagacttgcaaattgcgactatcatcttgctgatgatggtaaatggacttttgcagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG

upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 6
--acatgcttcatatcttcaccttaaaaccaggtcaacaatccaaaggatg-aaatgtttagtttgggcatgtgattttacatttgtttatttttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACCGTATGCTGAAGCAGTTTGTAGTAGCAGAACCTGAGATCCAG
   |||  ||    |  |   | ||  |  | ||  |   |  | || ||| |||  |  ||          |||   |||||| || |  |||     ||||| ||||||||||| ||||| ||  |||||||||||||||| ||||||||||| ||||||||||| | ||| || |||||||| |||||||||
ggtcatattttg-gtgattggcatattat-atgttgatt-tggatagtatgcaaacatgaagcccaaatggctgaaagtacattagtattctttgtctttcagGAACTTGGAGGGTGGGAGGAGTCTTAGCAATGTCTCGTGCTTTTGGTAACCGCATGCTGAAGCAATATGTTGTGGCAGAACCCGAGATCCAG
















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|6482466|gb|AW201723.1|AW201723
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|254347036|gb|GR856706.1|GR856706
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|14011351|gb|BG726273.1|BG726273
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|19348049|gb|BM892581.1|BM892581
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|7588767|gb|AW704555.1|AW704555
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|15337173|gb|BI497829.1|BI497829
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|16344154|gb|BI969749.1|BI969749
EST:     TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: TGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
EST: gi|208218594|gb|GE020546.1|GE020546
EST:     ATTGTAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAG                         GTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC
genomic: A-TG-AGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagataca ... ttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgaaatgtttagtttgggcatgtgattttacatttgtttatttttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACCGTATGCTGAAGCAGTTTGTAGTAGCAGAACCTGAGATCCAG
                                  tttgtttatttttct  CT-rich tract
                        tgattttacatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgcttcatatcttcaccttaaaaccaggtcaacaatccaaaggatgaaatgtttagtttgggcatgtgattttacatttgtttatttttctggtcagGTACTTGGAGGGTTGGAGGGGTGCTAGCAATGTCTCGTGCCTTTGGTAACCGTATGCTGAAGCAGTTTGTAGTAGCAGAACCTGAGATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
acatgct
- - - - - - -cttcacc
- - - - - - - - - - - - - ccaggtc
- - - - - - - - - - - - - - - - - -caatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtg