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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG

Basic information

species Glycine max
transcript GLYMA06G42830.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 8
---acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttg-ttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
   ||||   |    | ||   ||  |     |   | | || |    || |  |  | |    | ||     | |  | |  ||  |||| || | ||  |||||||| |||||||||||||||||  ||||||||||||| || |||||  ||||||| ||||| ||||| |||||||| |||||||| || || ||
gtaacttagcaatcaaacaaattatgctttgatgggaat-ttagcataatatt-agttctgaaattgtaataatgcaaaaatattcttttgattttgtggacagATTGGAATGTTCTGCTACAGTGGTATGACACCTGAACAAGTCGATCGCTTGACAAAAGAGTTCCATATCTACATGACTCGTAACGGGCGGATAAG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 8
acttccaacatcatcatcatacccaactgtccaagtattggtg--ccatgtcca----agtattg--gctagttgcttttctcacactttt--ctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
          | ||  |||   |   || |      |||| |   |||  | ||    | ||||   | |||||   |     | | |     | |     | | |||||||||| |||||||||||||||||  |||||||||||||||| |||||  | || || || |  |||||||||||||||||||| ||  | || ||
---------gttatgttcac-tcagtctctatggagattgatattccacattcagcctaatattattgttagttatatggtgaatattaaaaacgtaagcgtatttgcagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAGGTGGATCGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 8
acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtat-tggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
|  |||   |      || |  ||   ||   |  ||    |     ||   ||||| |||  |  |  | |      ||      |   | | ||| |||||||| |||||||||||||||||  ||||||||||||| ||||| ||| | ||||| || |  || |||||||||||||| || ||  | || ||
atgtccttgaaacatgtcctttccgg-tgcggatttacgttttgtgcgtattagtatgtggtgaacttgtatctctgaacaaagggtacatctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
  |  | ||| || ||  |||  |  || |      |||  ||  || ||      ||| ||          | ||  | | ||||| |  |     |||||||| ||||||||||||||||| || ||||| ||||||||||| ||  | |||| ||| | ||| || || |||||||||||||| ||||||||
-gtaactacaacaacaaaataggcttcttttgtgaaattcttgttatttctctcctttgactca--------cacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 8
--acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
  | |    |  |  |||   ||      |  |  | |  |  |  | | ||||  | ||    |  |||||    || || || ||   |  |     |||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||| || |||||||| |||||||| || || ||||| |||||
gtattgtagaatttgtcaatttatttgttttactcatt--tattttcctttccacat-ttcttcaaatgctta---cagaccttgctgattcttgcaaacagATTGGCATGTTCTGCTACAGTGGTTTGACACCTGAACAGGTTGATCGAATGACAAATGAATTTCATATCTACATGACTCGCAATGGTCGCATCAG

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|254345073|gb|GR851449.1|GR851449
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|22523470|gb|BU082281.1|BU082281
EST:     ACCTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|254340272|gb|GR858397.1|GR858397
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|57574406|gb|CX547381.1|CX547381
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|7693011|gb|AW761110.1|AW761110
EST:     GCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: GCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|10253391|gb|BE821157.1|BE821157
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|254320419|gb|GR826868.1|GR826868
EST:     ACTTAGAAAAGAAAGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|57574152|gb|CX547127.1|CX547127
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|254340271|gb|GR858396.1|GR858396
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|27425343|gb|CA936863.1|CA936863
EST:     AAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: AAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|7030016|gb|AW459799.1|AW459799
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|22523639|gb|BU082450.1|BU082450
EST:     ACCTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
EST: gi|14999882|gb|BI320696.1|BI320696
EST:     ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAG                         ATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG
genomic: ACTTAGAAAAGAAGGGGTCTACTTTGCCATGGCAGCATATAACTAATCAGgttcagttga ... atttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG
                         ttctcac  putative branch site (score: 2)
                      cttttctcacactttt  CT-rich tract
                                  ttttctttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG

- - ccaacat
- - - - - - - - -cataccc
- - - - - - - - - - - - - ctgtcca
- - - - - - - - - - - - - - - - - - -ttggtgc
- - - - - - - - - - - - - - - - - - - - - - catgtcc