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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG

Basic information

species Glycine max
transcript GLYMA08G19420.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36290.2 (Oryza sativa), 3'ss of exon 2
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttg-cagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
                                   | ||  |  |||| |      ||    |   ||  |  |     | |||     |   ||    |  | |||||||  ||||| |||||||| |||||||| || || |||||||| ||||| || ||| | ||| ||||||| || |||||||| |||||||||||||| || |||||||
----------------------------------gtggttatcctgaacttagtcttttcagcaaagcg-gtatgttcctcatagcttaacggatcaccttcctaatgtttaacagGCAGGTTTTGCTGGTGATGATGCACCAAGGGCCGTCTTCCCTAGCATTGTAGGGAGACCACGTCACACCGGTGTCATGGTTGGGATGGGCCAAAAGGATG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 2
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
                ||  |||      | ||| || | || ||     |   | |       ||       | ||||| | ||||   || ||||  ||         || |||| ||||| || || ||||| || || |||||||||||||| |||||| |||| || || ||||| |||||||| ||||| || ||||| ||||||||||
---------------gtctgattttctttttcttttt-tactcttacgtaatgtaatgtatgtcgtctcctgctgaatattacattacattacatttcatca--------tgtagGCTGGTTTCGCTGGGGATGATGCACCAAGGGCCGTGTTCCCTAGTATTGTTGGCCGTCCTCGCCACACCGGTGTTATGGTAGGAATGGGGCAGAAGGATG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 2
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
     |   ||     |     | ||     || |   | |  ||     || ||| |   | |    |   ||  |   ||| || ||   ||||||  | |||    ||  |||| || ||||| || ||||| |||||  | || || ||||| |||||  |||| || |||||||| || ||||| |||||||||||||| ||||||||||
--gtaattgtggccacttggcgtcatattctctgcagattcctttttttcaggcagctt-ttataatttaattttcagtcgatgttcat---tattttccccccatctcttatagGCTGGCTTTGCTGGAGATGATGCTCCCCGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGCCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatat-atattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
            |   |  | | | |  |       |   ||| |||         |||  |    ||||  ||| || |    | ||| | |     ||| ||||    ||  |||| || ||||| || |||||||||||  | || || ||||| |||||  |||| || ||||| || || ||||| |||||||||||||| ||||||||||
-----------gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccataca-gctt--ttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG

upper sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 1
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgctta----aatatgatattaatatat-attttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
                   | |  |    | ||  |||   |   || ||  |   | |  || ||| ||   |     | | |  | || | | || |    | ||| ||  | ||||||| || ||||| |||||||| ||||| ||||| ||||||||||||||| |||| ||||| || || || ||||| |||||||||||||| || |||||||
-------------------attaaactgattctgtttgctgtggcgaggtgaatt-tgcattcagtgattatctttgttagttttgttttcacacattaacgctgctcaaaaatgtgcagGCTGGATTTGCTGGTGATGATGCTCCGAGGGCTGTGTTCCCCAGTATTGTTGGCCGACCTCGACACACAGGTGTCATGGTTGGGATGGGCCAAAAGGATG

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|19269584|gb|BM885840.1|BM885840
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|209712712|gb|BW684642.1|BW684642
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|207787153|gb|GD756284.1|GD756284
EST:     GTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: GTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|7796620|gb|AW782017.1|AW782017
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|254348917|gb|GR852596.1|GR852596
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|7478918|gb|AW666456.1|AW666456
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|254325319|gb|GR838200.1|GR838200
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|19452328|gb|BM953738.1|BM953738
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|21888779|gb|BQ741992.1|BQ741992
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|213592306|gb|DB971546.1|DB971546
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|207690279|gb|GD672896.1|GD672896
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|21993760|gb|BQ785288.1|BQ785288
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|37997297|gb|CF808886.1|CF808886
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|13481730|gb|BG511073.1|BG511073
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|192294121|gb|FG986210.1|FG986210
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|209725128|gb|BW659810.1|BW659810
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|209709094|gb|BW658810.1|BW658810
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|213587883|gb|DB959707.1|DB959707
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|209728466|gb|BW654970.1|BW654970
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|254314534|gb|GR829527.1|GR829527
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|213588628|gb|DB957664.1|DB957664
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|10709340|gb|BF009064.1|BF009064
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|13477495|gb|BG507357.1|BG507357
EST:     AGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: AGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|213599978|gb|DB966466.1|DB966466
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCTGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|19934990|gb|BQ080020.1|BQ080020
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
EST: gi|254341929|gb|GR853066.1|GR853066
EST:     CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG                         GCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT
genomic: CTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAGgttagaacat ... atgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG
                      tattaat  putative branch site (score: 2)
            ttaaatatgatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatatatattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG