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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaaatccaatattagtattaactattattttggttcatattaataagttgctgctgattagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC

Basic information

species Glycine max
transcript GLYMA15G09410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 3'ss of exon 3
aattaaatccaatattagtattaactattattttggt-tcatattaataagttgctgctg--attagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
   |   |   ||  |||| |  |  | |   |   | || | |  |   || ||   |   |||    |  ||  | ||||    | || |  ||  ||||||||||||| ||| |||||||||| || ||||| || || || |||||||| || |||||||| || || || |||||||||||||| || ||||| ||||
---tgtctttgattgtagtttacataactcaatgaatctcttgtagaagtgtggcaaatacaattgaactctgtggcatgcttacatctgctttattgtgcagAGTTTTGAAGCTCTGAATCAGCGAGCTGTGGCAGTAGTGGTGGATCCAATTCAGAGTGTTAAGGGGAAGGTTGTGATTGATGCTTTCCGTTTGATAAATC

upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------aattaaatccaatattagtattaactattatttt----ggttc--atattaataagttgctgctga-ttagtatgagtaacttgctcctctatg-ttacat-catgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
                                                          |  |  |||||  |  ||  |      | ||     |||   | |    ||     || | || | | |   |||    |    |  |||  ||   |   ||||||||||||| |||||||| ||  | || || || || || || |||||||| |||||||| ||||| || || |||||||||||||| |||||||||||||
gtaagttaggcttgcactaactttcgttcttgcgttttgggtcccgaatgtgcaacggtggaaacaataccatgatctaacgcagtcttccatagttgggagaccggtatccccctccagaatcactgccagtgttctaaagcagtatccttgtgtatttgcagAGTTTTGAAGCTTTGAACCAAAGAGCGGTTGCGGTAGTGGTGGATCCAATTCAAAGTGTGAAAGGAAAGGTTGTGATTGATGCTTTCCGATTGATCAATC

upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 3
aattaaatccaatattagtattaactattattttggttcatattaataagttgctgctgatta-gtatgagtaacttgctcctctatgttacat-----catgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
          ||  ||  | ||   |  | || |  |||   |||  ||  ||||  |   || || | |     || ||     ||  | | |      |||||||||||||| |||||||||||  | || || || || || || |||||||| |||||||| ||||| || || ||||| |||||||||||||||||||| |
------tcttaaggtttcttttcttttcttttctatttctctttataaaaatgcttttaggtatgttttaccttttttctgtaacataattcttgtggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATCCAAAGTGTGAAAGGAAAGGTTGTGATCGATGCTTTTCGATTGATCAACC

upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S146_35V6.1 (Physcomitrella patens), 3'ss of exon 3
----aattaaatccaata-ttagtattaactattattttggttcatattaataagttgctgctgattagtatgagtaacttgct-cctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
    | || | | || |  |   | ||  || ||| ||      | |||| |   |  ||| || |  |  |   ||| ||    | | | ||| |    |  ||||||||||| |||||||||||  | || ||||| || || || |||||||| |||||||| ||||| || || |||||||||||||||||||||||||| |
gtacagttgagttcattggtcctttttgtcttttacttc--cctaaattattttttctctgttggtgtggttttctaatttaaaacttttgtgtga----acccagAGTTTTGAAGCTTTGAATCAAAGAGCTGTGGCAGTAGTGGTGGATCCAATCCAAAGTGTGAAAGGAAAGGTTGTGATTGATGCTTTTCGATTGATCAACC

upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33925 (Selaginella moellendorffii), 3'ss of exon 3
aattaaatccaatattagtattaactattattttggttcatattaataagttgctgctgattagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
                                        ||  |||   | |    | | |   | |  |   ||| |    | |  |   |  | ||||| ||||| |||||||||||  | || ||||| ||||| || ||||| || |||||||| ||||||||||| ||||| || || ||| |  |||| || |
---------------------------------------gtaagaatctatagaacttaagtttcacgttttctttgtttgctttttcttttttgt-cagAGCTTTGAAGCTTTGAATCAAAGAGCTGTGGCGGTGGTGGTGGATCCTATCCAAAGTGTGAAAGGCAAAGTCGTGATCGACGCGTTTAGGCTGATAAACC

upper sequence: GLYMA15G09410.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 3
aattaaatccaatattagtattaactattattttggttcatattaataagttgctgctgattagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
                                        ||  |||   | |    | | |   | |  |   ||| |   || | |    |  | ||||| ||||| |||||||||||  | || ||||| ||||| || ||||| || |||||||| ||||||||||| ||||| || || ||| |  |||| || |
---------------------------------------gtaagaatctatagaacttaagtttcacgttttctttgtttgcct-tttctttttgt-cagAGCTTTGAAGCTTTGAATCAAAGAGCTGTGGCAGTGGTGGTGGATCCGATTCAAAGTGTGAAAGGCAAAGTCGTGATCGACGCGTTTAGGCTGATAAACC

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|208235194|gb|GE034154.1|GE034154
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193381761|gb|FK346582.1|FK346582
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|208308188|gb|GE103610.1|GE103610
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193661367|gb|FK601705.1|FK601705
EST:     TGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: TGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|26046087|gb|CA783422.1|CA783422
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|207802024|gb|GD774248.1|GD774248
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193626565|gb|FK575743.1|FK575743
EST:     TTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: TTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|192311008|gb|FK004403.1|FK004403
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|192326436|gb|FK017708.1|FK017708
EST:     ATCCTGGATTTGGCTGTTGGCCCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193508464|gb|FK465747.1|FK465747
EST:     CTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: CTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193515771|gb|FK473347.1|FK473347
EST:     GATTTGACTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: GATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|208149393|gb|GD948895.1|GD948895
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|120496120|gb|EH224287.1|EH224287
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|8403627|gb|BE059261.1|BE059261
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|120495401|gb|EH223568.1|EH223568
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|208051158|gb|GD848131.1|GD848131
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACGGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|298184439|gb|HO029652.1|HO029652
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|298178788|gb|HO024523.1|HO024523
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACGGCAG                         AGTTTTGAGGCTTCGAATCAGCGTGCAGTGGCTGTGGTTGTAGA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGA
EST: gi|193301421|gb|FK266818.1|FK266818
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193649766|gb|FK596287.1|FK596287
EST:     TTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: TTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|207793524|gb|GD765668.1|GD765668
EST:     TGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: TGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|31467344|gb|CD409372.1|CD409372
EST:     GGTGTTGACATCCATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCCATA
genomic: GGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|298166786|gb|HO010225.1|HO010225
EST:     ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAAT
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAAT
EST: gi|192321561|gb|FK011791.1|FK011791
EST:     ATCCTGGATTTGGCTGTTGGCTCTCCGGTGTTGACATCAATACACAGCAG                         AGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
genomic: ATCCTGGATTTGGCTGTTGGCTCTCTGGTGTTGACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATA
EST: gi|193333780|gb|FK298326.1|FK298326
EST:     ACATCAATACACAGCAG                         AGTTTTGTAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAAT
genomic: ACATCAATACACAGCAGgttcaacttc ... catcatgcagAGTTTTG-AGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagttgctgctgattagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC
                      gagtaac  putative branch site (score: 2)
              attagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaaatccaatattagtattaactattattttggttcatattaataagttgctgctgattagtatgagtaacttgctcctctatgttacatcatgcagAGTTTTGAGGCTTTGAATCAGCGTGCAGTGGCTGTGGTTGTAGATCCAATACAAAGTGTTAAAGGCAAAGTGGTGATTGATGCTTTTCGATTGATCAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc