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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatccctactatgtgcgcag

Basic information

species Zea mays
transcript GRMZM2G395549_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatc-cctactatgtgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||  || |||||    |      |  |||||| |||||||| |||||  ||||   | | ||   || ||||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatc-cctactatgtgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||  || |||||    |      |  ||||||  ||||||| |||||  ||||   | | ||  ||| ||||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgt----------agtaatttttgtccatgt----tcgcgccgacgtctatttacatacagttta--ccatagtaaca--------tccctactatgtgcgcag---------------------------------------------------------
|||||||||| | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |           ||   |||| |  ||||    | | ||  |   |       | | ||  ||  |   | | |||        | | | |  | |  | |                                                          
TTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttcccctggggtttcttttttttatgtgaaatggggctaaaagcccaaggaaaagagactaaacaggaatgacacgaggggtttctttcgctatatgtattactggatgatttttcttccttttattgataaccattttttaatatttcccccctag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 26
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagt------aatttttgtcca---tgttcgcgccgacgtctatttacatacagtttaccatagtaacatccctactatgtgcgcag---
|||||||||  | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |  |         ||| || ||   | ||     |    |   ||| | | |  || |  ||| | |  |   || ||| | | |     
TTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttccactggggtttcgttcactatatttattactggatgatttttcttccttttaatgataatcat-tttttaatatttcccccctag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagttt--accatagtaacatccctactatgtgcgcag--------------------------
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||   |     |   ||         |||  | | ||   |||   |||||  |   | | |||  |||    |                            
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtct----atttacatacagtttacca--tagtaacatccctactatgtgcgcag-----------
|||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| |||||     ||    ||  ||| |  ||   |  |  | |    | ||  |    |   |  |  | |  || | || |   |||| ||             
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctat-ttacatacagtttaccatagtaacatccctactatgtgcgcag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   |||   || |||||     | | |  |  |    | || |||  |  |   ||    |   | | | |  ||
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcattttttttcatag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatccctactatgtgcgcag
 ||||| || |  || |||||  |||||||||| || || ||  | |||||||| ||||| ||||||||| | |||||  ||||||| ||||||||||| |||      |    |||    | |||     ||| |||       | |  |  ||  |||                       
CTGCCTGTTTACATGTTACGATTTGATCCGGCCCGACGTAGCATTGGAGCTTGCCTGGATAAACAACATGATCGACTTCTCCTTCCCTTACCTGTTACAAgta------agaccttggagttcttcctcatgacttctgacactttgctatcgactctag-----------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatccctactatgtgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA