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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgttacttttgttgcgcaataatgccattagcatatcagcagccattattatagggaggacatgtggttctttgtgttctttgtg...

Basic information

species Glycine max
transcript GLYMA08G24120.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 14
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagt-tactgcttatgttacttttgttgcgcaataatgccattag---catatcagcagccattattatagggaggacatgtggttctttgtgttctttgtg
| ||||||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||| ||||||| || ||  | ||||| ||||||||||| |  |   | |  | || |  ||    |||  ||   |  |     | ||     | ||  | | |      |       |   | |   | ||    
CTGCTGGTGGTGCCTGGGATAATGCTAAGAAGTACATCGAGACTGGCGCTCTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttttatcttttatgctctacttttcaaattctgttttgggggttgtttctaggactatgttcacacatttcatcaaaaatatgtagcaatatt----

upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 6
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact--gcttatgttacttttgttgcgcaataatgccattagcatatcagcagccattattatagggaggacatgtggttctttgtgttctttgtg-------
| ||||| || ||||||||||||||||||||||||||||||||||| |||||||| |||||||| || ||| | ||||| || ||  | ||||| || ||||||||| ||  |||| || |    | ||  | |  | || |  |  |      || | | |   ||     |||   ||   |||| |||                  
CTGCTGGCGGCGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGCGCTCTTGGTGGCAAGGGCAGCGAGTCCCACAAGGCTGCGGTTACTGGCGACACgtaagtttctcagcttttggtgtcctggtgac-cttttatactttggg---gctagaatctagagtt-----gagtttatactgttcgttggccaagacagagcaaaga

upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 14
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact-gcttatgttacttttgttgcgcaataatgccattagcatatcagcagcc-attattatagggaggacatgtggttctttgtgttctttgtg
| ||||| || ||||||||||||||||||||||||||||||||||| || ||||| ||||| || |||||| | || || || ||  | || || || ||||||||| || | ||||| |    ||  ||  |  ||||| | |    |  |  |      ||| ||     |||   ||   |||  |   |     |   
CTGCTGGCGGCGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGTGCCCTTGGTGGCAAAGGCAGTGAGTCCCATAAGGCTGCGGTTACAGGCGACACgtaagtttctagtttatgctctccttcgtgtcc--taatgacttgtatactttggggctagattcttgagctgagtttatactgttgatcaagcagagtaaa

upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 14
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgttacttttgttgcgcaataatgccattagcatatcagcagccattattatagggaggacatgtggttctttgtgttctttgtg
| || || ||||| ||||| ||||||||||| ||||| ||||| || || ||||| ||||| |||||||| ||||||||||||||  | ||||| |||||||||||   |  |  |  |||||      | || | |     |||   |        | |||  |     ||   ||| ||    ||   |         
CGGCGGGAGGTGCTTGGGACAATGCAAAGAAATACATAGAGACCGGGGCACTTGGGGGCAAAGGAAGTGAAGCTCACAAAGCAGCTGTGACTGGTGATACgtaagta--ttttcgttctacttc-aacactcattcaaa--gttatattcctgaatacgatttctcattagaattcatctgaaaattgtag---------

upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 15
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgttacttttgttgcgcaataatgccattagcatatcagcagccatta--ttatagggaggacatgtggttct-ttgtgttctt-tgtg-------------------------
|||| || ||||| ||||| ||||||||||| |||||||||||||||||||| |||||||| ||||||||  | |||||||| ||  ||||||| ||||||||||  |    | || || ||| || | | |          ||    | |||   | ||||   || ||   |  |  | | ||     ||| ||||  || |                         
CAGCAGGAGGTGCTTGGGACAATGCAAAGAAATACATTGAGACTGGAGCTCTAGGAGGCAAAGGAAGTGATTCCCACAAAGCTGCAGTAACTGGTGATACgtaagcaatctttcattttccttgtgcttcccttcttcttagttcctttctcattggtcatttccttttacttataaagtttagtcgaactgtcttctaatgagaaatcgttattctgaaaatggcaag

upper sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 14
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgttacttttgttgcgcaataatgccattagcata-tcagcagccattattatagggaggacatgtggttctttg-tgttctttgtg-
||||||||||||||||||| |||||||||||||| || ||||| || || |||||||||||||||||||| || |||||||| ||  | || ||||| ||||||||  |   |  || |  |  ||  | | | | |    | |  | |  ||  |     ||| |  | ||       | || | || | |  | |||    
CAGCTGGTGGTGCCTGGGACAATGCAAAGAAGTATATAGAGACGGGCGCGCTTGGAGGCAAGGGAAGTGATGCCCACAAAGCTGCAGTTACCGGAGACACgtaagtctc-attcctgct--tactggggggtagtcaaatgaatttcttgctcctcgtttgttaatccaagggtctatagcggctgttgggtaatgttttcca

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|58022630|gb|CX709371.1|CX709371
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|193570132|gb|FK524853.1|FK524853
EST:     TGGAGGACAAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: TGGAGG-C-AAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|209725686|gb|BW663177.1|BW663177
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|120529405|gb|EH257539.1|EH257539
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|21256880|gb|BQ453768.1|BQ453768
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGTTTTTTCAATCCATGTCCTTA
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTT-CAATCCATGTCCTTA
EST: gi|6200879|gb|AW152979.1|AW152979
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|58022340|gb|CX709081.1|CX709081
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|214004825|gb|DB988834.1|DB988834
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|213597487|gb|DB977794.1|DB977794
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
EST: gi|214008302|gb|DB989844.1|DB989844
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCTGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgttacttttgttgcgcaataatgccattagcatatcagcagccattattatagggaggacatgtggttctttgtgttctttgtg

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT