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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttcacatcacatagaaatgaaatagtttcttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG

Basic information

species Glycine max
transcript GLYMA17G14240.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g64020.2 (Oryza sativa), 3'ss of exon 5
----attcttcacatcacatagaaatgaaatagtttcttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG
    ||||||         |   ||| || || |    |    ||| || |   || |  | | |              |    |||||||      | |||||||||| ||||||||  ||||||||||||| |||||||||||| | || || ||  |||  ||||| | |||  | || |||||||| || || |||||  
gtaaattctttttcctttcttccaattaattattcgactgactatttgacatgtttttccccact----------cggtaatctttatgaac----aaatgcagCTGCCAGAGCCTTTCGGTTTCATTTTCACATGGTTTGCTGCTTTGCCTCTAATATTGTTCATAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCT

upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 7
lower sequence: AC203966.5_FGT002 (Zea mays), 3'ss of exon 6
attcttcacatcacatagaaatgaaatagtttcttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttg------agtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG
   || |   |    | || |  ||||| ||   ||  | | ||  | |    | |   |  |     || |         | || ||| ||       | |||||||||| ||||||||  | ||||||||||| |||||||||||| | ||||| ||  |||   |||| | |||| |||| || || || ||  | |||||| 
---ctgctggtt-tgtggataaaaaataattatctatgcttaagtcattg--gtcaaggtccacatccttcttctgttaactctgcattcttcttgaataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCACAGTCATTGACTAAGGCTATAGTCCAGGACTTTT

upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 7
attcttcacatcacatagaaatgaaatagttt----cttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG
  ||| |   |  |     ||  ||||  ||      | || |||| |  || ||    |   ||  |    | |      || || |  | |    | |||||||||| ||||||||  | ||||||||||| |||||||||||| | ||||| ||  |||   |||| | |||| |||| || || || ||  | || ||| 
tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgcatcttcttcaat----aatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT

upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 7
----------attcttcacatcacatagaaatgaaatagtttcttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagt-gcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG
          | | || ||    | |||  ||    |      ||  |  |  |   || ||||||   || ||  | | ||         | | |||  |||||| |||||| | ||| || || |||||||||||||| ||||||||||| || ||||||||  | ||| || ||| | || | || ||    ||| | ||||| ||| 
gaaaaaacaaacttttgaccattcttagtcattgcttctcacatttaaagtctggttatcttatta---tttattgattcat--------ctgtaaatcattgagttgcagCTCCAGGAACCATTCAGTTTCATTTTCACGTGGTTTGCTGCAGTGCCCCTCATATTTTGGCTATCTCAGACAATTACCAAATTTATTTTGAAAGATTTTT

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|193499357|gb|FK462104.1|FK462104
EST:     TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG                         CTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
genomic: TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAGgtatgttccc ... ttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
EST: gi|9258401|gb|BE346548.1|BE346548
EST:     TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG                         CTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
genomic: TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAGgtatgttccc ... ttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
EST: gi|6718461|gb|AW306108.1|AW306108
EST:     GATCACATATCTGCTAGAG                         CTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
genomic: GATCACATATCTGCTAGAGgtatgttccc ... ttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
EST: gi|9259613|gb|BE347760.1|BE347760
EST:     TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG                         CTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
genomic: TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAGgtatgttccc ... ttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
EST: gi|192317109|gb|FK007862.1|FK007862
EST:     TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG                         CTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC
genomic: TCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAGgtatgttccc ... ttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG
                       ttataac  putative branch site (score: 2)
     ttattacaattaatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttcacatcacatagaaatgaaatagtttcttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG

- - - cacatca
- - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - agaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg