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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcacacttatccaatttcaatgcagattatatcattaagtttataagttttttaagctttgtaatgtttgtgctctttgtacttgaaaactgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT

Basic information

species Glycine max
transcript GLYMA06G16940.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------------------------tctcacacttatccaatt------tcaatgcagatta-tatcattaagtttataagttttttaagctttgtaatgtttgtgctctttgtacttgaaaact-gttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT
                                                           |||||     ||| ||      ||||| |   | |  |||  |   || | |  ||| ||    ||   ||| | ||  |   ||| ||   |||  | |||||||| || ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctg-acaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT

upper sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
tctcacacttatccaatttcaatgcagattatatcattaagtttataagttttttaagctttgtaatgtttgtgctctt-tgtacttgaaaactgttgca-gGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT
                                        ||   |    | |    |||||    ||| |||    |  |||   ||     |||   | || || || ||||||||||| ||  | |||||||||||||||||||| || || || || || || ||| | |||||||| |||||||| |||||||| ||
----------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

upper sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13811 (Selaginella moellendorffii), 3'ss of exon 10
tctcacacttatccaatttcaatgcagattatatcattaagtttataagttttttaagctttgtaatgtttgtgctctt-tgtacttgaaaactgttgca-gGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT
                                        ||   |    | |    |||||    ||| |||    |  |||   ||     |||   | || || || ||||||||||| ||  | |||||||||||||||||||| || || ||||| || || ||| | |||||||| |||||||| |||||||| ||
----------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCTCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

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|192295216|gb|FG986935.1|FG986935
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
EST: gi|9258683|gb|BE346830.1|BE346830
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
EST: gi|6914981|gb|AW396511.1|AW396511
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
EST: gi|10252774|gb|BE820540.1|BE820540
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
EST: gi|57575336|gb|CX548311.1|CX548311
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
EST: gi|26047917|gb|CA784557.1|CA784557
EST:     CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTG                         GCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG
genomic: CTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactc ... actgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttttttaagctttgtaatgtttgtgctctttgtacttgaaaactgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT
     tttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcacacttatccaatttcaatgcagattatatcattaagtttataagttttttaagctttgtaatgtttgtgctctttgtacttgaaaactgttgcagGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
-ctcacac
- - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg