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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA

Basic information

species Glycine max
transcript GLYMA20G25650.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 3'ss of exon 4
--gtacatttctgaaccttg-gaatgttttct---ctgtccttctta--tcacattggaatactgaaacctattgctaaatgcac-cagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
   |||  | ||     |||   || | |  |    |  | |  ||   |||   || |  |   ||    |      | |     ||||  |||||| ||| ||||| || ||||| ||||| |||||||| || ||||||| |||||| || ||  | ||||| ||||| |||||||||||||||||
gtatacgatgctctcatttgtagatatctattgaagttacatctttggttcatgctgaaccatataatttaaccatagagtttgtgcagGGATTCTATATTCGGTACTTATAACTGCTGTGATTACTGATGCAATTAAGGATGGTGTTGGTCGTCCTCGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 3'ss of exon 3
-----gtacatttctgaaccttggaatgttttctctgtccttcttatcacattgga--atactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
         | |     |  | |  || | |    |  |  | | |     || |   || |||||    |    |   || || |||  |||||| ||| || || || ||||| ||||| |||||||| || ||| ||| |||||| || ||| | ||||| ||||| |||||||||||||||||
gtatatggtactctcatatgtagatatctatcaaattacactttcacttttttagttcatgctgaactggacactt---tgtac-agGGATTCTATATTCGGTGCTTATAACTGCTGTGATTACTGATGCAATTAAGAATGGTGTTGGTCGCCCACGCCCAGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G024615_T05 (Zea mays), 3'ss of exon 4
-----------gtacatttctgaaccttggaatgttttctctgtccttcttatcacat-tggaatact---gaaacctat-tgctaaatgcac------cagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
            |  |||      |||| || |  ||  |  || |     |  |||| |  | |||     |||| ||| ||  ||||| |        |||  ||||||  || || ||||| ||||| ||||| |||||||| || ||||||| ||||||||||||  | ||||| || |||||||| |||||||||||
gtagtttacatatttattgtgattccttcgattcattgattagtacaagagaaaacatatccagtacaagaaaaacgtatctgaaaaatggaaattttgtagGGATTCTATACTCAGTGCTCATAACTGCAGTGATTACTGATGCAATTAAGGATGGTGTTGGACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G050658_T01 (Zea mays), 3'ss of exon 4
gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
    |||    |   ||   ||   |||  | |  |  |||  |||   ||  |    | |  |     ||||     |||  ||||||  || || || || ||||| ||||| |||||||| || ||||||| ||||||||||||  | ||||| || |||||||| ||||||||| |
--gtattatacatatttatgatcccttcaatatgttgattagtaca--agagaaacacatctgaaatggaaattttgtagGGATTCTATACTCAGTGCTGATAACTGCAGTGATTACTGATGCAATTAAGGATGGTGTTGGACGGCCTCGTCCAGATTTTTTCTGGCGCTGTTTCCCTAA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
gtacatttctgaaccttggaatgttttctctgtccttcttatca-cattgga-atactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
|||||||       || |  |  ||  || | ||    ||||||  |||    || |||||| |||   ||        |||| || |||||||| ||||| |||||||| ||  | |||||||| || ||||||| |||||| || ||| | || || |||||||||||||| ||||||||
gtacattcactt-tctcgccagattcactat-tctactttatcaatattacttattctgaaatcta--acttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G447433_T08 (Zea mays), 3'ss of exon 5
gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
     |  ||||   |   ||  | || | ||||  | | |     ||    ||     | ||  |   ||||     |||  |  | | ||| || || || ||||| ||||| |||||||| || ||||||| |||||| || ||  ||||||| ||||| ||||||||||| |||||
----gtacctgacattctaaacatgttatttgtcaat-tgacagttttaatttatgttgaact--taaaaaatatgt-agGTATCTTGTATTCAGTGCTTATAACTGCTGTGATCACTGATGCAATTAAGGATGGTGTTGGTCGCCCTCGGCCAGATTTCTTTTGGCGTTGTTTTCCTGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 3'ss of exon 2
---gtacatttctgaaccttggaatgttttc--tctgtccttcttatcacattggaatactgaaacctattg-ctaaatgcac-----cagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
     || |||      | | || |  |||   || |    | || |  | |||   | |        || |  ||  ||  |      |||||||||||| |||||||| || || || || || |||||||| || || ||||||||||| || ||  | ||||||||||| ||||||||||||||| |
gtatcactttttcccttcctagatttctttgagtcaggtactgttgtttccttgtggtgcattgcttaatggattatgtgtgcatgtttagGCCTTCTATTCTCTGTACTGATCACGGCAGTTATAACTGATGCAATTAAAGATGCTGTTGGCCGACCTCGTCCAGACTTCTTTTGGCGTTGTTTCCCTAA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ17723 (Selaginella moellendorffii), 3'ss of exon 2
gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacc-------tattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
|||   || |    |||  |    | ||||   ||     |  |  | ||| ||   ||||        | ||| |   | |  ||||| | || ||  | || || |||||||| ||  | |||||||| ||||| || || |||||||| |||||||| || ||||||||||| ||||| || ||
gtaagcttatttttctttcatctctctctcgaaccaagagaagagctcggactaagtaaactatgttgttcttgttttttactacagGCTTGCTTTTCGCGGTGCTTATTACTGCTGTTCTTACTGATGCGATCAAAGACGCAGTTGGACGTCCAAGGCCTGATTTCTTCTGGCGGTGTTTTCCAGA

upper sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16251 (Selaginella moellendorffii), 3'ss of exon 2
gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacc-tattgctaaa-------tgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
|||   || |    |||  |    | ||||   ||     |  |  | ||| ||   ||||  | ||| |          | |  ||||| | || ||  | || || |||||||| ||  | |||||||| ||||| || || |||||||| |||||||| || ||||||||||| ||||| || ||
gtaagcttatttttctttcatctctctctcgaaccaagagaagagctcggactaagtaaactatgttgttcttgtttttttactacagGCTTGCTTTTCGCGGTGCTTATTACTGCTGTTCTTACTGATGCGATCAAAGACGCAGTTGGACGTCCAAGGCCTGATTTCTTCTGGCGGTGTTTTCCAGA

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|151413050|gb|EV282858.1|EV282858
EST:     TTACTATTTCATTCGTAAGGATGTCTATGACCTCCACCATGCTATAATGG                         GCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGG
genomic: TTACTATTTCATTCGTAAGGATGTCTATGACCTCCACCATGCTATAATGGgtacatttct ... aatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgtccttcttatcacattggaatactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA
                                        tgctaaa  putative branch site (score: 2)
          ttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttctgaaccttggaatgttttctctgtccttcttatcacattggaatactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT