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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG

Basic information

species Zea mays
transcript GRMZM2G078756_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------------------------------atgtgct-gtgtgtttgttcttcagatt--cgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
                                                                                        ||  || || | | | || ||||||||  || ||| |||  |  ||| || ||  | | |   | || |   || ||||||   |  |  |  | |||||||||||||||||||||| |||||||| |||| ||||| || |||||||||||||||||||| |||||||||| |||||| |||||  ||||||||||||| |
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtg-tactttgaaccatatgattattg-ctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 3
-atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttct-tcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
    |   ||| |||||  ||   | |  ||   | |      |   |  | |    |  | ||  |    |||||  | || ||   || | | | ||||||||||||||||||||||||| |||   |||||||||||  |||| || ||||| || || ||  | ||   ||| || || || ||||| || || ||||
ttgataaggtg-gtttgaactctggttgggtttctttgtgacaatcttcttgtagaattttgttgaggtcttggctc-cttacaatctttttcttgttgcagAATTTTGATGATGTCTTGGTTCCTGAAGACCATGTAAGTAGGAGCTATAATGATACTTACTACATAGACCCTCAGACTGTTTTGAGGTGCCACACAAGTG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 2
-----atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
     || |   |    |  |   ||  |       |  ||||    |   |  |   |  |  | | ||   |||      ||   |||| | ||||  ||||||||||||||||||| ||||| ||| |||| ||  | ||  ||||||||||||| ||||| ||  |||||  |||||| ||||| |||||||| |||||||
atcctatttatagcacatgagagatttggtcaatgtctgcttccaaaattcttattcatatt--tctatgaattcttat--gccagaaaatatacttc-ttgcagAATTTTGATGATGTTTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGATCCTCAAACTGTCTTGAGGTGTCACACCAGTG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 2
atgtgctgtgtgtttgttcttcagattc--gtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
   |  | | | |  |   |     ||   ||  || |       |||   | |     |  |||  ||   |   |   | | |||| ||  |   ||||||||||||||||||||||||| ||| |||| ||  | ||  ||||||||||||| ||||| ||  ||||   |||||| ||||| ||||| || || ||||
--atcttatttataaggcatgggagttttggtcaatgtctgcttccaaaattcttatccatatttctgtgaattcttatgccagaaattttacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 2
atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagt-ttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
   | || | | |  |   |  |  || |  ||   || |   | | | |   |     | |||   |   |   |   | | |||   |  |   ||||||||||||||||||||||||| ||| |||| || || ||  | ||||||||||| ||||| ||  ||||    ||||| ||||| ||||| || || ||||
-gatcctatttataaggcatggaagtttggtcaatgtctgcttccaagattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACGTCAGTAGAAGTTACAATGATACATACTACATTGACTCCCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 1
atgtgctgtgtgtttgttcttcagattc--gtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
   | || | | |  |   |     ||   ||  || |       |||   | |     |  |||   |   |   |   | | |||   |  |   ||||||||||||||||||||||||| ||| |||| ||  | ||  ||||||||||||| ||||| ||  ||||   |||||| ||||| ||||| || || || |
--atcctatttataaggcatgggagttttggtcaatgtctgcttccaaaattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGGG

upper sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 3
-----atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
     || |     |  |  |   ||  | ||    |  ||||    |   |  |   |  |  | | ||   |||      ||   || | | ||||  ||||||||||||||||||||||||| |||  ||| || || ||  ||||||||||||| ||||| ||  | ||   |||||| ||||| ||||| || || | ||
atcctatttataaggcatgggagttttggtttatgtctgcttccaaaattcttatccatatt--tctatgaattcttat--gccagaaagtctacttc-ttgcagAATTTTGATGATGTCTTGGTTCCTCTTGATCACGTCAGTAGGAGTTACAATGATACATACTACATCGACTCTCAAACTGTCTTGAGGTGCCACACTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG
                          ggctgac  putative branch site (score: 3)
                                          ttcttcgct  putative PPT
                                  tataaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgctgtgtgtttgttcttcagattcgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG

- gtgctgt
- - - - - tgtttgt
- - - - - - - - - - - - - - gtacatc
- - - - - - - - - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgacc