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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctacccaatcaccaaaaaaacataaataatgccttaccctcccacatgttgttcccaaaatattaatgctttatttgttgttgatgtatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTCTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA

Basic information

species Glycine max
transcript GLYMA19G34380.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0141g00290.t01 (Vitis vinifera), 3'ss of exon 2
cctacccaatcaccaaaaaaacataaataatgccttaccctcccacatgttgttcccaaaatattaatgctttatttg-ttgttgatgtatgcaatgc-aagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTCTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA
   | |   | | |  | ||| ||||  ||    ||        |      |||   |  || || |    |  | || || || || | |    |   |||| |||| || ||| ||||||||||||||||||||||||||||||||| |||  ||||| |||||  | | |||| |||| ||||| || || ||||| ||
--gatctcgtaatcttataaagataatgaagatattgtgtctatattaagggttataagcatgtttaattatggtatgattctttatttttattttttgaagGGAATTATGGATCACAAGGAATGAAGGATTTCATGAATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGA
















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|9440021|gb|BE440532.1|BE440532
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151405703|gb|EV275517.1|EV275517
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|16346301|gb|BI971896.1|BI971896
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCCTGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|8825818|gb|BE209548.1|BE209548
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151412951|gb|EV282763.1|EV282763
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAAGGATTTCATGAATGAGAGCAAGCTG
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAA-GGATTTCATGAATGAGAGCAAGCTG
EST: gi|9204440|gb|BE330664.1|BE330664
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|192303187|gb|FG997763.1|FG997763
EST:     TTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: TTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|213600363|gb|DB970299.1|DB970299
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|209707048|gb|BW661554.1|BW661554
EST:     CGAGAGCTCTCTGATTCTTNAGGCAAAATGTTCAGCTCCTTCACCTTTNG                         GCAAT-GTGAATCCNNAAG-AATGAAGGATTNCATGAATGAGAGCAAGCT
genomic: CGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTT-Ggtaattaatt ... gcaatgcaagGCAATTGTGAATCCC-AAGGAATGAAGGATTTCATGAATGAGAGCAAGCT
EST: gi|209700152|gb|BW656269.1|BW656269
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|57574134|gb|CX547109.1|CX547109
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|14126638|gb|BG791076.1|BG791076
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAA
EST: gi|9259241|gb|BE347449.1|BE347449
EST:     CCGAGAGCTCTCTGATTCTTTAGGCANAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|151409764|gb|EV279572.1|EV279572
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTCCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|12772578|gb|BG237569.1|BG237569
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|209707049|gb|BW661555.1|BW661555
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGA
EST: gi|192303186|gb|FG997762.1|FG997762
EST:     CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTG                         GCAATTGTGAATCCCAAGGAATG
genomic: CCGAGAGCTCTCTGATTCTTTAGGCAAAATGTTCAGCTCCTTCACCTTTGgtaattaatt ... gcaatgcaagGCAATTGTGAATCCCAAGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttgttcccaaaatattaatgctttatttgttgttgatgtatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTCTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA
            aaaatattaatgcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctacccaatcaccaaaaaaacataaataatgccttaccctcccacatgttgttcccaaaatattaatgctttatttgttgttgatgtatgcaatgcaagGCAATTGTGAATCCCAAGGAATGAAGGATTTCATGAATGAGAGCAAGCTGAATGATCTCTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
cctaccc
- - - - - caccaaa
- - - - - - - - -aaaacata
- - - - - - - - - - - - - - - - ccttacc
- - - - - - - - - - - - - - - - - - - -ctcccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttg