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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcatatgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG

Basic information

species Glycine max
transcript GLYMA17G00830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 5
gtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcata-tgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG
                                                                                     | |  | |||      || | |  ||||  |  |  | ||  |||  |   |||  | ||   |  ||   ||  ||  |    | | |||       ||||||||||||||||||| || ||||||||||| || ||||| | |||||| || || |||
------------------------------------------------------------------------------------aaagttgatagtctgacttctatg-ctgtcctccaggttttctcttgtttacttatcttttctcaacaaaaaattctgaagaagctatgcaa-------tttttgcagTTTCATTCCAGTTATATGATCTCAAGCAACAAGGCTATATTGAGAGACAAGAG

upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
gtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcatatgttgggcat---ttccaacttttct-tttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG
                                                                                                   | |||  | |||||   ||||    | | ||| ||  ||  || ||  |     ||            ||   |||  ||| | |  |  ||||||||||||||||| | ||||| ||||| || ||||| || |||||||| ||||||
----------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgc-ctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG

upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaatgacaaatgtttagaagactttagctatg-tggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatg--ttttgtttctgtagtttatttatt--tccttaatgcattagttattaatagtaat--gcatatgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG
|||||  |   |  |  | ||| |||   |    |  | || |   | | | | || ||     |  |  ||||        |       |  | | | |||  ||| ||||       |||| |  |  | | | ||| |||   |  | ||  | ||     |||||| || ||  |||| |  | | ||||||||||||||| ||| |||||||||| || || ||||| || |||||||| ||||||
gtaag--ttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagacaatttggtttatgactttagtttactactcttatcttctacttcctgatg-atttcatgctgatgcttattgatgtatgtttgggatg-ccaaatcatttcttttgcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG

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|15812919|gb|BI785194.1|BI785194
EST:     AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG
genomic: AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG
EST: gi|9820145|gb|BE555655.1|BE555655
EST:     TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG
genomic: AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG
EST: gi|19054016|gb|BM732683.1|BM732683
EST:     AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG
genomic: AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG
EST: gi|151412447|gb|EV282259.1|EV282259
EST:     AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAGCCAGGTTTTATTGAAAGGCAGG
genomic: AGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttattaatagtaatgcatatgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG
     tattaat  putative branch site (score: 2)
                              catttccaacttttct  putative PPT
     tattaatagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatgacaaatgtttagaagactttagctatgtggtctacttttttatctgggttttgaataggaagagcatttattggagagggagctagatcatgttttgtttctgtagtttatttatttccttaatgcattagttattaatagtaatgcatatgttgggcatttccaacttttcttttttgcagTTTCATTCCAATTGTATGATCTCAAACAGCAAGGTTTTATTGAAAGGCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG