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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcttgcattagttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG

Basic information

species Glycine max
transcript GLYMA04G33480.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
-gtaatctcttgcatta-gttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
  | | ||  || |||  |||  ||   ||  |||   | ||            || ||  |  |||  || |    || | | |||||||          || || |||||||||| ||||||||||| ||  |||| ||  ||||||| || |||||||||||||| ||| |  |||| ||
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagt-ggatatttt--------gtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG

upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatctcttgcattagttcttgtctat-tgaccctaa-aaactcgtgcttctgtttaactagttttggct--ctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
|| |  |||    ||       ||  |  | |||| ||  ||    |     ||| |  || | ||  |    || |  |  |||   ||   |   || || ||||| ||||||| ||||||||||||||||| |||||||||||||  ||||| |||||||||||||| ||  || || | ||
gtgagatctctgcttgtgcagagttaagataaccccaatgaaagtttagccatgtctctcttgattatgtaaactgatcttcttgttaatcgctccctgcca-ttttgcagATGGTGGGTGATTTCTTTGACCAATTGAAGTCGAGAACCAAGGGATATGCTAGCATGGAATACTCCGTTATTGG

upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 16
----------------------gtaatctcttgcattagttcttgtctattgaccctaaaaactcgtgct---tctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaat-----tttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
                        | |  |||  || |  |    |  | |   |    ||| |  |  |   |||   ||| |  |||||||| |  |    |||||| || |    | |  |      ||   ||||||| || ||||| ||||| ||| ||||||| |||||||| ||||||||||||||||| ||  | ||| | ||
gtaccttttcctattcaatcatccacttgctttgataaactgaaatgcagttgactagtaaattaatattgggtctccctaatt--ttttggctgttgatagattgaattttctctggttttgaaattcattcacagATGGTAGGAGATTTTTTTGATCAGCTGAAGTCCAGAAGTAAAGGTTATGCTAGCATGGAATACTCTTTTCTGGG

upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 16
gtaatctcttgcattagttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggc--tctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
                                                   ||  |      |   ||  | ||   |  ||||||    || ||  |   ||| |||||||||||| ||||||||||| || ||||||||  | || ||||| || || |||||||||||  || ||  |||
---------------------------------------------------gtacagtactctcaagcattttcttctgcttgaatgccgtttaacat---tttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTACGCGAGCATGGAGTACTCCATTACCGG

upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 16
gtaatctcttgcattagttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
                                           || |     | | |  ||  || |||      |  ||||||    || ||  |   ||| |||||||||||| ||||||||||| || ||||||||  | || ||||| ||||| |||||||||||  || ||  |||
-------------------------------------------gtacagtactctca--agcatttgcttc----tgcttgaatgccgtttaacct---tttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTATGCGAGCATGGAGTACTCCATTACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG
 gtttaac  putative branch site (score: 3)
                       tatttgaatatttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcttgcattagttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA