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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttctactacatcacttgcacgggagaaatatagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA

Basic information

species Glycine max
transcript GLYMA13G08090.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 3
gtaagattttctactacatcacttgcacgggagaaatatagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                                                   |     |||   || | |  |   |||| |  |  |  | |  | || |||||    || |    |    | |||||||||||||||| ||||||||||||||||| ||||||||  | ||||| || ||| |||| |||||| | ||  ||||| || | ||||| || ||||
-------------------------------------------------gttggaaaattttccttcagacctcttgttgtcta--tcagttgttctattttaaacgtttcttt--tctgttgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCAGAGTTCATGACAAATACAAAATTAGCAATAA

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g43100.1 (Oryza sativa), 3'ss of exon 3
gtaagattttctactacatcacttgcacgggagaaatatagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                                                   | || ||||   ||      || |  | ||  |  | |  | ||  |   ||| |   ||||  |||    | ||||||||||||||| | |||||||||| |||||||| ||||  | ||||| |||||  |||| |||||    ||  | || ||| | ||||  || ||||
--------------------------------------------------gttagagatttacctttcaaacacc-ataatatatatgtattcattcaaactaaaattctttatcatt----atagGTCATGGTGGTTCACATGCTGCTGAGCATTTAAAGAAGCACTTATTTGAAAATCTTCTGAAACATCCGTCATTCATCACTGATACAAAATCAGCAATAA

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 3
gtaagattttctactacatcacttgcacgggagaaatatagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggta-atatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                                                   | ||||||| |  ||  |     ||||| |    | || ||  || ||  | ||| | || ||    | |   |||||||||||||||| ||||||||||||||||| ||||||||  | ||||| || ||| |||| |||||  | ||  ||||| || | ||||| ||  |||
--------------------------------------------------gttagtgatttc-ttctagacatcctgttgtc---tcttagtgcatctatctgaatcatttata----ttctcgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCGGAGTTCATGACAAATACAAAATTAGCATTAA

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagattttctactacatcacttgcacgggagaaatatagttctataat-ctcagtgattgcactcc----tgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                              |  | ||    |  |||||| |||||  |  | |        |||| |  || | |  | ||||  |  | || | |   ||  |||||   ||   ||||| ||||||||||| ||||||||||| ||  | ||||| || || ||| | |||||| ||||||||||| | |||||||||||  ||||  ||||  |||
----------------------------tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctcttctaatatctgaagctttaa---tcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttctactacatcacttgcacgggagaaata-tagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggtaatatactttaata-----aattttaaaat-tccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                                 ||| | ||  || || || | |    |     | |  | | |   ||||| |      | ||   | |  | |      |||| | | || |||  |||||||||||||||||||||||||| |||| ||| ||||||||||| ||||| ||| |  ||||||||||| | ||  ||||| || |||||||||||||||
---------------------------------aaacactaaatccatgattttaagcttcttttttccttcctttccttatgaaaagaatgaaaaggattcaagtgtttacaattatgagatgtcctaacagGTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAA

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|207839768|gb|GD810857.1|GD810857
EST:     TTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
genomic: TTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
EST: gi|120531892|gb|EH260025.1|EH260025
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTA
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTA
EST: gi|7640592|gb|AW734820.1|AW734820
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCAT
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCAT
EST: gi|298196173|gb|HO044564.1|HO044564
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
EST: gi|254313836|gb|GR831465.1|GR831465
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
EST: gi|209700604|gb|BW670420.1|BW670420
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
EST: gi|151411248|gb|EV281059.1|EV281059
EST:     GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATG                         GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA
genomic: GACATTGAAGATTGGTGGCCAATCAATATGCTTATTTGGAATATTTGATGgtaagatttt ... ttccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
                           ctttaat  putative branch site (score: 4)
              ttttggtaatatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattttctactacatcacttgcacgggagaaatatagttctataatctcagtgattgcactcctgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG