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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttgggcttctcatggatggccatcatatgtgtacgtcattgtaggaatcatatattttattgtatgtgcag

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 3
AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgt--gagttgggcttctcatggatggccatcatatgtg-tacg-tcattgtaggaatcatatattttattgtatgtgcag
|||||||||| ||||| ||||||||||| ||||| |||||||||||  ||||||| |||||||| ||||||||||||||||||||||||||||| || ||||  ||    |  ||||||||||| || ||   ||| | |||   |||  || ||||  |||  |||   |||  | |||
AACTTGTTGCAAAGCTTTACAAGCATACTTTGAAACGTTCTGAACTGAGAGATGAGCTCTTTGCACAGATTTCAAAACAAACACGTAACAATCCCGACAGgtatgaagcagatttctcatggatagcaattcgatgggatacaaccatcttatgaatgttattattt---gtacttacag

upper sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 5
AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttgggcttctcatggatg-gcca----tcatatgt----gtacgtcatt-gtaggaatcatatattttattgtatgtgcag-----------------------------------
| |||||||  || || |||||||| |  ||||||||||| ||||| |||||||||||||||| |||  | |||||||||||  | ||||  ||||| ||||   |  |  |  |||    || | ||    |||| | |    | || |  ||  | | ||    ||||||  |    | ||||                                    
AGCTTGTTGGTAAACTATACAAGCAAAGTTTGAAGCGTTCAGAACTCCGAGATGAACTCTTTGTCCAATTATCAAAACAAACGAGAAACAGCCCTGAGAGgtatctaagtttcttcagtagtgtgtcacgcttcatgttttcttggactttgttcattgaaactgaatatttgctgtggtttgcatgctagtgattaatactgttttggtctaaaaagcag

upper sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 4
AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagt-tgggcttctcatggatggccatcatatgtgtacgtcattgtaggaatcatatattttattgtatgtgcag-----------------------------------------------------
| ||||||| ||| || || ||||| || || |||||| | || || ||||| ||||| ||||| ||||||||||| |||||| | || |||||||||||||  |      | | |  | |   |   |   || |  | | |    |   |     |  | | ||||   |||||                                                      
AGCTTGTTGGGAAACTGTATAAGCAAACTTTAAAGCGTCCAGAGCTCCGAGACGAACTTTTTGCACAGATTTCAAAGCAAACAAGGAATAATCCTGATAGgtatgcacattccttttctagtatgatgtttgattttcatgac-ccattccatctgcacttctaattgctggtgcaaggactaaccttatttctttaatcatgctacctttattgcttctgaaaacacag

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: 48 (upstream exon), 49 (downstream exon)
Score: 163

AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttggg ... gtatgtgcagGGGTTGGTCAATAAGAGCTTGGGAGCTTATGTACCTGTGTGCATCATCCATGCCACCAAGCAAAGATATTGGGGCATACTTGTCTGAGTATGTTCACTTT


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 29

AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttggg ... gtatgtgcagGGGTTGGTCAATAAGAGCTTGGGAGCTTATGTACCTGTGTGCATCATCCATGCCACCAAGCAAAGATATTGGGGCATACTTGTCTGAGTATGTTCACTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttggg ... gtatgtgcagGGGTTGGTCAATAAGAGCTTGGGAGCTTATGTACCTGTGTGCATCATCCATGCCACCAAGCAAAGATATTGGGGCATACTTGTCTGAGTATGTTCACTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

AACTTGTTGCGAAGCTCTACAAGCATACGTTGAAGCGTTCTGAACTTCGAGATGAACTCTTTGCCCAGATTTCAAAACAAACACGTAACAATCCTGATAGgtgagttggg ... gtatgtgcagGGGTTGGTCAATAAGAGCTTGGGAGCTTATGTACCTGTGTGCATCATCCATGCCACCAAGCAAAGATATTGGGGCATACTTGTCTGAGTATGTTCACTTT