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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG

Basic information

species Zea mays
transcript GRMZM5G819035_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 2
gtatgcatgcacacacggtaatg-tgatgctccaatctttgcg---tccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
||||  ||||  |    | |||| || | || |  || | |||   || ||||||  |  | || |||      |||    ||  |    |  ||   ||| || |||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||||| |||||||| ||| ||
gtata-atgcg-atgttgcaatgatgtttcttctttcatggcggactcggtagaacgcgatctgattggcatgtttgctgttcttggcaatgcgcc-cgcgctgcagCATCTACGGTCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCTGAGACGGTGAAGCTGATCTTG

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
gtatgcatgcacacacggtaatg-tgatgctccaatcttt----gcg---tccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgc-----ggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
||||  |     |    | |||| || | || |  |||||    |||   || |||| |  |  | || |||      |||  | | ||  ||||| |||| ||     | || ||||||||||| || || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||||| |||||||| ||| ||
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttg--cattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
-gtatgcatgcacacacggtaatgtgat----gctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
  |||   |||  |        ||| |     ||| | |           ||  | |   | |  |  ||   | |     || | | || | |       | || ||||| || || ||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || ||||||||||| |||||||| || || 
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
-gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggt-gtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
  |||   ||   |     |||  |  |   |     |  | || | |||      | |   | ||   | |     ||     || |||    ||  || | ||||| || |||||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || |||||||||||||||||||| || || 
gttattattgtttaggtt-taactttgttaactggggtcagtgtgcatag----ttggtcaatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 3'ss of exon 2
-gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggt-gtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
  |||   ||   |     |||  |  |   |     |  | || | |||      | | | | ||   | |     ||     || |||    ||  || | ||||| || ||||| || || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || |||||||||||||||||||| || || 
gttattattgtttaggtt-taactttgttaactggggtcagtgtgcatag----ttggtcgatggcagaaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCTGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatg-cggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
                                  | ||    |   | | ||||| ||   |    |   | ||   |  |   |   |||||||  |||| || |  |  || |||||||| |||||| | || || |||||||||||| | ||||| |||||||| |||||| | || |||||||| ||||||  ||| |||
---------------------------------gtattactcttgtttggaacccattcattcttcttgttggatgttgtctacttaaagcaatggtggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
-gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccg-----tagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggt-gtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
  | ||    ||       | |  || | ||    | | |||    |     | | ||   |   | || ||     |  |     ||||  || |   ||  || | ||||| | |||||||||||| || ||| | ||||| || ||||||||| | ||||||||||| || |||||||| ||||||||||| |||||||||||  ||
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG

upper sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcatgcacacacggtaatgtga---tgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
   |   |||  ||  | |  |  ||   | || |||| || | || |||         ||| |||     | ||| |    | |||| | |            || || |  || |||||||| || ||| | || || |||||||||||| | |||||||| |||||||| |||||||| || ||||| |||||||||||  | 
--gtaattgc-tacgtgttggttggaaatttcttcaat-ttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttga------------agTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
                    acttgac  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA