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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctatgatccttagtcattattcaagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA

Basic information

species Glycine max
transcript GLYMA15G00880.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 20
gttagctatgatccttagt-cattattcaagactgta-tttggtttgcaactaat-----caatttcaatcttctcgg-ccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
|| |  ||| |   | | |   ||||||  |  |||| |||  |  |||  ||||     ||||||| || |  | |  |||  | ||||||||||| || ||||||||||| |||||||||||||  ||||||||||| ||||||||||||||||||||||||||||| || |||||||||||| | |
gtaatgtataaaaataaatattttattcttggatgtagtttcatgagcatataatttgaccaatttctatttctttgaaccatatgcagACAATGACTACTTTCATGCCTCCACCACCTGCAGCAACATTTCTTGCTTTCCATCCTCAAGATAACAATATTATTGCTATCGGGATGGATGATTCTACAA

upper sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
------gttagctatgatccttagtcattattcaaga----ctgtatttggtttgc---aactaatcaatttcaat------cttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
         |  |     | ||  | |||||| || |    || |  | |   |||   |||    || ||   |       ||||         | |||   ||||||||||||||||| || || || ||||| | ||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||| |||||  | |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
-----------------------------------------------------gttagctatgatccttagtcattattcaagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                                                     || ||    | |   |  |   || |   ||| ||  |   |||  |      |  |||   |||||           |||   ||||||||||||||||| || || || ||||| | ||||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||  | |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttt---tcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 20
gttagctatgatccttagtcattattcaagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                      ||| |     |||   |  ||  | | | || ||    |   || |||       |||||  |||||   ||||||||| || || || |||||||  || || |||||||||||||| ||||| ||| |||||||||| || ||||| |||||  | |
---------------------gtatgccgatttgttgctttttctccagtgatgaa----accattgtcgaa-----acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTA

upper sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 20
gttagctatgatccttagtcattattcaagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                      ||| |     |||   |  ||  | | | || ||    |   || |||       |||||  |||||   ||||||||| || || || |||||||  || || |||||||||||||| ||||| ||| |||||||||| || ||||| |||||    |
---------------------gtatgccgatttgttgctctttctccagtgatgaa----accattgtcgaa-----acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                    aactaat  putative branch site (score: 2)
                       taatcaatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctatgatccttagtcattattcaagactgtatttggtttgcaactaatcaatttcaatcttctcggccaagtacagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAAATTTTCTTGCTTTTCATCCTCAAGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA