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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaattgtctaacag

Basic information

species Glycine max
transcript GLYMA17G03560.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgta------acttttccaaaatttagtttatgcagcaa--tatcatttga--tgaaaaaattgtctaacag----------------------
|| ||  |||| ||||||||||| ||||| ||||||||  | ||||| |||||||||||||||||||||||||| |||||||  |    | | || |         |||     | || ||   ||    |    | |  |||||  |     | || | | | |                       
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttat-gcagcaatatcatttgatgaaaaaattgtctaacag---------------------
|| ||  | |||||||| ||||| ||||| ||||| ||  | |||||||||||||||||||||||||| ||||| || ||||  | | || |    | |  ||||   |  ||  | ||| ||  | || |   || ||   | | ||| || | |                      
GTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTGgtacattgcaaatctgtttagatttc---atcttcttctatcgctcctatgttgctt-atcgtatagttgcctgataagtaattcctatgaaaatgtag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaactt-----ttccaaaatttagtttatgcagcaatatcatttgatgaaaaaat--tgtctaacag---
|| ||  |||||||||| ||||| ||||| ||||||||| | |||||||| |||||||||||||||||||||||||||||||  ||  |  |  | |  |||     |||    |    | ||||   |     |  | |||||   |  |  | |  ||  |   
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttat-tggtgtacttgtctgatgttgacttcctattcaaatgtag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaa-----gtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaatt---gtctaacag---
|| ||| ||||||||||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||||||     ||| | ||   | |   || ||||   |  |   |   ||  |   |  ||  | ||  ||||    |||| |      
GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggta--actgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaattgtctaacag---------------------------------------
|| || || || || || || |||||||| ||||| ||  |||||||||||||||| || ||||| ||||||||||| ||||| ||||   |   || |  |  | | ||    |  ||  |       |    ||  |     ||   ||   |  |                                       
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgtaaatggttttatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctttattaaactctatgcatctacttgtgttggctag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtgg-taactgatgtaacttttccaa-aatttagtt-tatgcagcaatatcatttgatgaaaaaattgtctaacag----------------------
|| ||  | || || || ||||||||||| ||||| ||  |||||||||| ||||| |||||||| ||||||||||| ||||| ||| | |    |   |   | | || |||  | |  |||    |  | |   ||  |||      | |  |||                        
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaa-----tatcatt--tgatgaaaaaattgtctaacag-----------------------------------------------
|| || ||||| || || || ||||||||||||||||||||||||||||||||||| || || || ||||| ||||| ||| | |  |  ||  |||   ||   | || |  ||  | | ||  |      |  ||||  || | |   | |    ||   |                                               
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt-ctactgtg--ttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagt-tta----tgcagcaatatcatttgatgaaaaaattgtctaacag-------------------------------------------------------------------
|| || || || ||||| || || |||||||||||||||||||||||||||||||| || || || ||||| ||||| |||  ||  ||   ||      |  ||   | |  ||   ||    || |   ||| ||||  ||  | |  |  | ||                                                                       
GTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGGgtgggtcata--cgaccctgttcctcgggattgaagcgctaacattggattcataacattatattcatatttattttattgattatgggcaatctcactcgtcccagtttctcacataaaatcgatatgcgttggttttttatgaacag

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaattgtctaacag
|| |||||||| || || || || ||||||||||||||  ||||||||||||| ||||||||||| || || ||||||||||| |    |  ||   |  ||||     || |          |   | || ||||  |                 
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaa-tctcgagagagacatgttttgtgtgatgtgaccgtgatcgtg-tctcttttgcag-----------------

upper sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaattgtctaacag
|| |||||||| || || || || ||||||||||||||  ||||||||||||| ||||||||||| || || ||||||||||| |    |  ||   |  ||||  |  || |          |   | || ||||  |                 
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaa-tctcgagagaaacatgttttgtatgatgtgaccgtgatcgtg-tctcttttgcag-----------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaatatcatttgatgaaaaaattgtctaacag

- - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA