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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

Basic information

species Glycine max
transcript GLYMA15G12780.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 7
-----atttcttttttatt-ttatatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
     |||| | ||  |||   |||| |   || |||     |  ||| |     |   | ||||||  ||  | |  |  | |||||       |  |  || ||||||| |||||| || |  |  | || |||||  |   |||  ||| || |||| |  ||||||||||| ||||||||| |||||||||||| || 
gtaaaatttatattccattgccatatct---tcgtttatgcaatccttgttttgttaataaatactaattgcgagtggtactgatatgc----tgttatatcaaagGTTGCTTGTGCACTGTTGCTATCTGGAGAGGACTTGACCAAATATGGTGCTGTAGAAGACATTCTTGTTAAGATGGGAATATACTTTCAAGTCCAA

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 6
-----attt-cttttttattttatatttgattcattttcaatagtcttatcacactggaatat-actatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
     |||| |  || |  | |  ||||  | ||| || || | ||| |   |  |    |   | ||  ||| ||   |    |||  ||| |     |  |  ||||||||||||| |||||  |  | |||||| || | || |||   | |||||| |||||||||||||| || ||||| |||||||| ||||| |||
gtaggatttaccattctcctatggattttttccatctttaa-actctcacttcggtaatctgcgaatagttgtcatcactagcaata-atatttttctttatccaagGTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 6
-atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
       || ||  | |||||   |||| || ||| |  |||    |   | | || | | || ||||   | |  | ||| || ||| |||| | || |||||||||||||||||||  |||| |||||| |  | || |||  ||||||||||||||||||||| ||||| |||||||||||||||||||| |||
gtaagagttattgctctatat---attc-ttctcagtcatctgg--atgttagcattt-caatttgttgagtgtggtaataagtttctactccattca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 6
atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatacta-tctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
       |   | ||   | |  ||  |||      |||| | |   |    |  || ||| | || |   | |  | | | ||  || |||||  || |||||||||||||||||||  |||| |||||| |  | || |||  ||  |||||||||||||||||||| || |||||||||||||||||||| |||
------gtaagagttaccactctatatattcctctcagtcat-ttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctca-agGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168681_T02 (Zea mays), 3'ss of exon 5
------atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatat-actatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
      |    ||||| |  || |         |||||||   | |    ||  || || ||| | || |  ||   | | ||  |    ||       |  || |||||||||||||  ||||  |  | || ||| || | |||||  ||| ||||||| ||||||| |||||||| |||||||||||||||||||| |||
gtaattaaccttttttaaacttttgcacatactattttcatctgaccc-ccat-ctagattatgaataccacttgaatgtgttactg-acatgctgctttatcaaagGTTGCATGTGCCCTGCTGCTCTCTGGCGAGAATTTGGACAATTATGGTGATGTAGAGAACATCCTTGTTGAAATGGGAACATACTTTCAAGTCCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 6
atttcttttttatttta-tatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctcctta-----cacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
       ||  |  ||  |||||| |      |  |||   ||   |  ||   | | | | |  ||   || |   || | ||     ||  |||     | |||||||| || ||||||||||||||||| ||  || | || ||||||  |||||| ||||   |||||||||| |||||||  |||||||||||||||
------gttaaacattgctatttgctaggcaattgataacatttaaagtctatgaaacattttaagtctgttgtgaacagaggtcctcactgattattgcactcagGTTGCTTGCGCATTGCTCATGGCGGGAGAAAATTTGGAAAACCATACTGATGTGAAGACTGTTCTTGTTGACATGGGAATTTACTTTCAAGTACAG

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|193512996|gb|FK470544.1|FK470544
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
EST: gi|7233280|gb|AW568628.1|AW568628
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
EST: gi|7926518|gb|AW832544.1|AW832544
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
EST: gi|9565120|gb|BE474629.1|BE474629
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
EST: gi|14259182|gb|BG882090.1|BG882090
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTT
EST: gi|193487733|gb|FK452714.1|FK452714
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTT-ACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGA
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGA
EST: gi|193615774|gb|FK561987.1|FK561987
EST:     ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCC-TTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: ATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
EST: gi|193453892|gb|FK421201.1|FK421201
EST:     TACAAGACTGCATATTATTCCTTTTACCTTCCG                         GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT
genomic: TACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtatta ... ccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG
                                            tccttac  putative branch site (score: 2)
                                   tgtatctcctcctt  CT-rich tract
       aatatactatctgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcttttttattttatatttgattcattttcaatagtcttatcacactggaatatactatctgttatttatcttcatatgtatctcctccttacacagGTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - atcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatctg