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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttgcagaagcatggtgttcaggacatgcattacttaatttattttttggcccgtccatttgactaacagttcttattgtctggactacaatgtagGATTTAATTGTGGTGAAGCTGCCAACTTTGCAACTCCACAATGGTTAAAATTTGCTAAAGAGGCTGCCGTACGAAGGGCTGTGATGAATTATCTTCCGAT

Basic information

species Zea mays
transcript AC149475.2_FGT005
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC149475.2_FGT005 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g05680.1 (Oryza sativa), 3'ss of exon 3
--catgtttgcagaagcatg--gtgttcaggacatgcattacttaatttattttttggcccgtccatttgactaacagttcttattgtc-tggactacaatgtagGATTTAATTGTGGTGAAGCTGCCAACTTTGCAACTCCACAATGGTTAAAATTTGCTAAAGAGGCTGCCGTACGAAGGGCTGTGATGAATTATCTTCCGAT
   |||    ||| ||||||   |||||||    |  ||| |||| |||||||| | ||   | |||   |    ||  ||| ||  || || | || |||  |||||| |||||||| ||||||||||| ||||| ||||| |||||||| || ||||||||||||||||| || |||||||||||||||||||||||||| ||
ccaatgcagtcagcagcatgtcatgttcag----tagattccttattttattttgttgct-atgcatgctatcggcaactctaatgttcgtgtaatataatacagGATTCAATTGTGGAGAAGCTGCCAATTTTGCGACTCCCCAATGGTTGAAGTTTGCTAAAGAGGCTGCAGTTCGAAGGGCTGTGATGAATTATCTTCCAAT

upper sequence: AC149475.2_FGT005 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G35350.1 (Glycine max), 3'ss of exon 5
catgtttgcagaagcatggtgttcaggacatgcattacttaatttattttttggcccgtccatttgactaacagttcttattgtctggactac-------aatgtagGATTTAATTGTGGTGAAGCTGCCAACTTTGCAACTCCACAATGGTTAAAATTTGCTAAAGAGGCTGCCGTACGAAGGGCTGTGATGAATTATCTTCCGAT
        ||  |   |  |  ||    | |  | |   |  ||   | | |  | | || |||      | | |||||||| | |  || |        |||  ||| ||||| ||||| |||||||| ||||||| ||||||||||||| | | | | ||||| || ||||| ||||| || ||||  ||||| |||||||| ||
------cacactactttttttatccac-cctatactgtcttgttaggtctctttctcttcaattgtcaacataattcttattttatataccatttggtgaaatcaagGTTTTAACTGTGGGGAAGCTGCTAACTTTGGAACTCCACAATGGCTTAGAGTAGCTAAGGAAGCTGCAGTACGCAGAGCTGCAATGAACTATCTTCCCAT


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttggcccgtccatttgactaacagttcttattgtctggactacaatgtagGATTTAATTGTGGTGAAGCTGCCAACTTTGCAACTCCACAATGGTTAAAATTTGCTAAAGAGGCTGCCGTACGAAGGGCTGTGATGAATTATCTTCCGAT
                    gactaac  putative branch site (score: 1)
                             ttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtttgcagaagcatggtgttcaggacatgcattacttaatttattttttggcccgtccatttgactaacagttcttattgtctggactacaatgtagGATTTAATTGTGGTGAAGCTGCCAACTTTGCAACTCCACAATGGTTAAAATTTGCTAAAGAGGCTGCCGTACGAAGGGCTGTGATGAATTATCTTCCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- tgtttgc
- - - - - -aagcatg
- - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctgg