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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctatgatccttggtcattattcaagactgtatttggtttgcaactaataatctatttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA

Basic information

species Glycine max
transcript GLYMA13G44420.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 20
gtgagctatgatccttggt-cattattcaagactgta-tttggtttgcaactaat--aatctatttcaatcttctcgg-ctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
|| |  ||| |   |   |   ||||||  |  |||| |||  |  |||  ||||   | | ||||| || |  | |  | |  ||||||||||||| || ||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| || |||||||||||| | |
gtaatgtataaaaataaatattttattcttggatgtagtttcatgagcatataatttgaccaatttctatttctttgaaccatatgcagACAATGACTACTTTCATGCCTCCACCACCTGCAGCAACATTTCTTGCTTTCCATCCTCAAGATAACAATATTATTGCTATCGGGATGGATGATTCTACAA

upper sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
------gtgagctatgatccttggtcattattcaagactgtatttg--------gtttgcaactaataatctatttcaatcttctcggctaa--gtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
         |  |     | ||  | |||||| || | |   | ||        | ||| |  |   | |         |    |||| |     | |||   ||||||||||||||||| || || || ||||| ||||||||||| || ||||| || || ||||| || ||||| ||||| ||||| |||||  | |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
---------------------------------------------gtgagcta-tgatccttggtcattattcaagactgtatttggtttgcaactaataatct-atttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                                              | |  |  |||     | |   | ||    | | |     |||  ||| |  || ||| |      |||||     |     |||   ||||||||||||||||| || || || ||||| ||||||||||| |||||||| || || |||||||| |||||||| || ||||| |||||  | |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 20
gtgagctatgatccttggtcattattcaagactgtat-ttggtttgcaactaataatctatttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                                 ||||   | ||||   ||  |  || | |        |   |   |   ||||  |||||   ||||||||| || || || |||||||| || || |||||||||||||||||||| ||| |||||||||| || ||||| |||||  | |
---------------------------------gtatgccgatttgttgctttttctccagtgatgaaaccattgtcgaa-acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTA

upper sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 20
gtgagctatgatccttggtcattattcaagactgtat-ttggtttgcaactaataatctatttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                                 ||||   | ||||   ||  |  || | |        |   |   |   ||||  |||||   ||||||||| || || || |||||||| || || |||||||||||||||||||| ||| |||||||||| || ||||| |||||    |
---------------------------------gtatgccgatttgttgctctttctccagtgatgaaaccattgtcgaa-acagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTA

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|192325091|gb|FK019052.1|FK019052
EST:     TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAG                         ACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT
genomic: TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAGgtgagctatg ... ctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT
EST: gi|298178455|gb|HO024190.1|HO024190
EST:     TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAG                         ACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT
genomic: TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAGgtgagctatg ... ctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT
EST: gi|17964569|gb|BM271302.1|BM271302
EST:     TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAG                         ACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT
genomic: TGTCAGCATCAGGAGGGAAGATTTCTCTGTTCAATATGATGACTTTTAAGgtgagctatg ... ctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgtatttggtttgcaactaataatctatttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA
                 aactaat  putative branch site (score: 2)
                    taataatctatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctatgatccttggtcattattcaagactgtatttggtttgcaactaataatctatttcaatcttctcggctaagtgcagACAATGACGACATTCATGCCTCCGCCACCTGCAGCAACTTTTCTTGCTTTTCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCTTCCA

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