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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag

Basic information

species Zea mays
transcript GRMZM2G091121_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||| || |||||   ||      |  |||||| || ||||  |||||  ||||   ||    |  | ||               
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcag------------

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||| || |||||   ||      |  ||||||  | ||||  |||||  ||||   ||    |  | ||               
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgt----------agtaatttctgtccatgt----tcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag-------------------------------------------------------
|||||||||| | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |           ||   || | |  ||||    | | |   |   |       | | ||     | || ||   | | |  |   | | |  || | ||                                                            
TTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttcccctggggtttcttttttttatgtgaaatggggctaaaagcccaaggaaaagagactaaacaggaatgacacgaggggtttctttcgctatatgtattactggatgatttttcttccttttattgataaccattttttaatatttcccccctag

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 26
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaac--atccctactgtgctatgtgactgtgtgcgcag
|||||||||  | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |  |    |  |     ||||    | |  | ||||     ||  ||    |        ||    |   |  | |   | |     |  ||
TTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttccactggggtttcgttca---ctatatttattactggatgatttttcttccttttaatgataatcattttttaatatttcccccctag

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag----------------
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||         |   || | |     |||  | | ||   |||   |   | |  |     || || |   |     | | |                    
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgt-acgtagtaatttctgtccatgttcgtgtcg-acgtct--atttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag-
|||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| |  |  |   ||||  || |||   | ||  |  |    | ||  |    |  |      |  |  |  | |    || || | || | |  |    
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   ||    || |||||   | | |      || || || ||   |||  |  |    | ||||| | || |   |   |      
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggc------tttcaaatcgtcttcattttctctcaaccactgttc-attttttttcatag----

upper sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag
 ||||| || |  || |||||  |||||||||| || || ||  | |||||||| ||||| ||||||||| | |||||  ||||||| ||||||||||| |||   ||   ||   || | |  || || |  |    | ||   ||| |  ||  |||                                    
CTGCCTGTTTACATGTTACGATTTGATCCGGCCCGACGTAGCATTGGAGCTTGCCTGGATAAACAACATGATCGACTTCTCCTTCCCTTACCTGTTACAAgta---agaccttggagttcttcctcatgacttctgacactttgctatcg--actctag------------------------------------

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 154

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 102

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag

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