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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattcttactttatgcattttattcttattagtgcttgcaaatgaaacaaattgatggctgcgctatcttactacag

Basic information

species Zea mays
transcript GRMZM5G876621_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattcttactttatgcattt-tattcttattagtgcttgcaa----atgaaacaaattgatggctgcgctatcttactacag
||||||||||||||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| | | || || | | |   ||| |  ||||  |||  ||||||     ||    |   |   |   ||  |||| | ||  |||
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataac-gcag

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagc------attcttactttatgcattttattct--tattagtgcttgcaaatgaaacaaattgatggctgc-gctatcttactacag---------
| ||||| ||||| ||||| |||||||||||||| || || ||||| ||||| || ||||| || || ||||| |||||||| ||||||||||||||||||||||       | |  |   |||  ||   |  | |  | | ||   ||     |  |     |  ||   | | |  |||| |||             
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagttgataaagtggttgattaaacaaaatgctataatgtcagaagttatgcttttattctctctatacttcctgtaatctaactctgaattggattc

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattcttact-ttatgcattttattcttattagtgcttgcaaa---tgaaacaaattgatggctgcg-ctatcttactacag-------------
||||||| ||||||||||| || || || ||||| || |||||||| || || || ||||| ||||||||||| || ||||| ||||||||||| ||||||||||  |   |||| || | |    ||  || |   ||  ||   |    ||      |||      ||   | |  |  | |||              
CTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttatatactcttgttctagatagactcacatgtatttaggaggtctggtctttattccattttgtatccacttggcaacactagcattatcaag

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 9
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcatt------------------cttactttatgcat---------tttattctta--ttagtgcttgcaaatgaaacaaattgatggctgcgctatcttactacag-------------------------------------------------------------------------------------
| ||    || || ||||||||||| ||| |||| || ||||| ||||| || ||||||||||| || ||||| ||||| |||||||||||||| |||||||||| | |                  || |  | ||| ||         || |||||||  ||| |  ||  | |   | | | || | |  | || |   | |||                                                                                         
CGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagtaatggataatttcaattgaatctaaagtcatggatggatcatgattcattcttaccttaat-tttatagacacagctacttaa-gtttacgttgcttcactctgagtatgttgacaccagtggttggtaagtctatcacttataagcaaccaaatttattcactcagttttatttatgcgtttttgacag

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagc----------attcttactttatgcattttattctta-ttagtgcttgcaaatgaaacaaattgatggctg-cgctatcttactacag--------------------------------------------------------------------------
| ||    || || || || ||||| ||  | || ||||||||||| || || |||||||| || || ||||| ||||| |||||||||||||| ||||||||||           ||||||||||||   |  |||   ||| ||| |       | |   |  |||   ||   | | | ||  |  ||  |                                                                          
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattcttactttat------------gcattttatt----cttatt--agt---gcttgcaaatgaaacaaattgatggctgcgctat---cttactacag---------------------------------------------------------------------------------------------
| ||    || ||||| ||||| || ||  |||| ||||| ||||| || || |||||||| ||||| ||||||||||| ||||||  |||||| ||||||||| || | | |  | ||            |  |||||||    ||||||  |||   |||||  || |||  |||||      ||| |  |   || |  |  |                                                                                             
CAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAGTTTTGCTGgtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgctcattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcacttacaagagttcactgatactataacag

upper sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattctt-actttatgcattttattcttattagtgcttgcaaatgaa-------acaaattgatggctgcgct-atcttactacag---------------------------------------------------------------------------
| ||    || || || |||||||| ||| |||| ||||| ||||| || || || |||||||| || ||||| || || |||||||||||||| ||||||||||  |  |  | |||||    | |      || | ||  |  ||||  |       ||  || |||    |  || |  ||  |   |                                                                           
CAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAGTTTTGCTGgtaagtctaatagattttattgggtctcgaggaatgaatgggtttaaattcactctccaactcatcgataatggttcttaagtttttgttgctttagcctgaatgggttgaaagctggtcattgataagacacttacttatgagcaacccacttttgtttctaaag

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), 48 (downstream exon)
Score: 111

CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattc ... cttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 95

CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattc ... cttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattc ... cttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 120

CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattc ... cttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG