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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG

Basic information

species Glycine max
transcript GLYMA19G40930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
----ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgc-tcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG
    ||   ||| |   | |||  || | ||   | |  ||||    |||    || |  |  ||     |  ||  ||   | |  |  || | ||     |||||| || ||||| ||||||||||||||||| || ||||||||||| || || || || || | ||||
cctgtttccatgatggcgaatag-gtggttgacctatgcactagggaata----gggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG

upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10880.1 (Arabidopsis thaliana), 3'ss of exon 2
ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG-----------------------------------------------------------------------------------------------------------------------------
                               || ||| | |     | |||  || |||| |||      || | | |  | ||     |||    ||||||| || ||||| |||||||||||||| ||||||| |||||| || || || || || ||||  |||                                                                                                                             
-------------------------------gttaaccagtgggc-taatgttacgttgt-tagatgggagtttagcgaccctaccccattta---tcaggagccgtgagttcctttggcaagaaggacacactgattttgctaccaaagaagaggctgatgaggaggtgcttgatgtttgaacatctacagCCGCGTGTATGACTCATGGAGATGACAAAGGTTTAGTATTCCCTCCTAAAGTGGCACCTGTTCAAGTTGTTGTAATCCATGTTCCCATCAAAGGCGCTGC

upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
-ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggt--gctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG
 | |  || |  |  ||| ||     |  | | |    ||||  || |||   ||  |||| ||||   |  |  |    | | | | |  |  || ||  |||||||| || ||||||||||| || ||||| ||||||||||| |||||||| || ||||||  ||||
ttcatgatcgactatgattctccaattcct-tatttgttaat--atgttaaaaaatcttgtttagttgttcattggcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG

upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S7_175V6.1 (Physcomitrella patens), 3'ss of exon 4
-ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG
  |  | | | |||  ||   | || || |   || |    |  | | | ||| | ||  |  |    |   ||    |    |     ||    || ||||||||| || ||| | ||||||||||| || ||||| ||||| ||||| || ||||||||||  |||
tgttttgttgatttttatctgggtgttgattgttacatccttgcagagt-tggtatttacttaaaaaaaaattgattcgagtgtttcgcttcactttgcagGAGTCGTGAATTTTTATGGCAAGAAGGTCATACTGCATTTGCTACAAAAGAGGAAGCAGATGTCGAG

upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15689 (Selaginella moellendorffii), 3'ss of exon 4
ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcata-gaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG---------------------------------
                                                  | | |||   || |    |  |   | | | ||| | | || |  |||||||||||| |||||||||||||||||||| ||||| |||| |||||| ||||| ||||| ||||  ||                                  
--------------------------------------------------gtagcttctcctcgattctctttctgagatgatacgtaattctcttttcagGAGTCGTGAGTTTCTTTGGCAAGAAGGCCACACCGCTTATGCAACCAAGGAAGAAGCGGATGAGGAAGTGTATGCGGTGCTTGATCTCTATCGAAGAGTG

upper sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ38227 (Selaginella moellendorffii), 3'ss of exon 4
ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcata-gaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG---------------------------------
                                                  | | |||   || |    |  |   | | | ||| | | || |  |||||||||||| |||||||||||||||||||| ||||| |||| |||||| ||| | ||||| ||||  ||                                  
--------------------------------------------------gtagcttctcctcgattctctttctgagatgatacgtaattctcttttcagGAGTCGTGAGTTTCTTTGGCAAGAAGGCCACACCGCTTATGCAACCAAGAAAGAAGCGGATGAGGAAGTGTATGCGGTGCTTGATCTCTATCGAAGAGTG

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|193369070|gb|FK334792.1|FK334792
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGNAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193522640|gb|FK478677.1|FK478677
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193430919|gb|FK398149.1|FK398149
EST:     GTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: GTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193659280|gb|FK605947.1|FK605947
EST:     AGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: AGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193616813|gb|FK569243.1|FK569243
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTACAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193385256|gb|FK352718.1|FK352718
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|7591393|gb|AW707127.1|AW707127
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAATGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|9899427|gb|BE608395.1|BE608395
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193325700|gb|FK288534.1|FK288534
EST:     TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: TGGTGCAATGTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
EST: gi|193429100|gb|FK397646.1|FK397646
EST:     GTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA
genomic: GTTGTAAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatggaactttgtctagtccattgtgtggtgctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG
                                           ttttgat  putative branch site (score: 4)
                                           ttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggtgctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG