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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG

Basic information

species Glycine max
transcript GLYMA18G20800.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 11
gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
               |  ||  |||     | | ||  || | | |     | ||    | |    | ||||   | || | |            |||||||| || |||||  | || || || ||  |  |||| ||||||||||| ||||| ||||||||||| || |||||||| |||
-----------gtatacttgctact-acgatgcatctgtgtaactttcttcggttcacgactgg--gaatattgttgttaactatacactgcatctgcagGTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATG

upper sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
-gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
  |   || || ||  |    |   || | ||   |   ||| |   |   ||   |||||  ||  |   ||||||  | || | |  |||   | ||||||| ||||||||||||||||||||||||||  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||
gataatgaaataaaaaaatatttctttattttctatttttga-tatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG

upper sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 12
-gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacat--gcttatttattttttgca-tatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
 |    |  |    |   ||   | |  || || |   | | |||  ||  |  | | ||  | ||  ||   ||||   |    ||    |||     | |||||| ||||||||||| || ||||||||| || | ||||||||||| || ||||| ||||| | |||||| ||||   | |||
gggattgttagagtttgcgttgtagtcttaatatggtgaggtatctcaatgtttgttcatgcaattgctgtggtatgctcacactttcctcggag----tccagGTATGTATTTGGAGTTACTCACATTCCTAGACTTGAAGACTGGCCAGTAATGCCTGTGGAGCACATTGGATTCAGTTTGATG

upper sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
------gtggcgacatcaatcaggtgtca----cttgtat-tacgtccatgaatcc----taacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
       | |  || | | |   | ||      | | ||| | ||||  |||| |     ||| |||||||  |  ||| ||||       |||||||||          |||||||| ||||||||||| || ||||| ||| || ||||||| ||||| |||||||| ||||| | |||||| ||||   |  ||
cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgca-------atttatttgag--------tgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG

upper sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcata-tgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
                          ||| ||| || | | |||      | |||  |   || | ||| | | ||    |  | | | ||      |||||||||||||||||||||||||||| ||| |  | || || ||||| || ||||| ||||| ||||| || ||||  || | |
--------------------------gtaatac-tcta-ggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG

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|58018333|gb|CX705075.1|CX705075
EST:     ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
genomic: ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
EST: gi|193555657|gb|FK513204.1|FK513204
EST:     ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGAGTGACACATATTCCTCGATTGGAAGACTGGCCTGTTAT
genomic: ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
EST: gi|21678404|gb|BQ630755.1|BQ630755
EST:     GGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
genomic: GGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
EST: gi|21601716|gb|BQ612047.1|BQ612047
EST:     ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGNCTGTTAT
genomic: ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
EST: gi|192326053|gb|FK016220.1|FK016220
EST:     TTGGGGTTAAGCAAAACCCGATCATTGGAGGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTA
genomic: TT-GGGTTAAGCAAAA-CCGATCATTGGAGGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTT-GGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTA
EST: gi|192322691|gb|FK014382.1|FK014382
EST:     ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTG                         GTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
genomic: ACTTGGGTTAAGCAAAACCGATCATTGGAGGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTAT
EST: gi|23729679|gb|BU762941.1|BU762941
EST:     GGAAGCTGATATAGTTCTTTG                         GTACGTATTTGCGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTA
genomic: GGAAGCTGATATAGTTCTTTGgttagttcat ... aatgttgcagGTACGTATTTG-GAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
 tcctaac  putative branch site (score: 1)
        ttatttattttttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - tgtcact
- - - - - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - -cctaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgga