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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttcatcagctgaatttgtggtattgtgaaaactgaatttacggagctactagatgatattaattttcattgaaacatgatatacaatccttagt...

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 5'ss of exon 14
TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttcatcagctgaatttgt-------------ggtattgtgaaaactgaatttacggagctactagatgatattaattttcattgaaacatgatatacaatccttagt
 |||| |||||| | || || |||||||| || |||||||||||||| ||||| || ||||| |||||||||| || || ||||| |  |             | |  |||||   || | ||| | |   | |||  |||  || |||||   ||||   || | |||          
CCATATGCTGCAGCAAAGGCTAGAGAATACCTCGACAAGCCTGCTTTGCATGAAACAATGGTTAAGgtatttt-caccacctgaactcatacagttgtatcatgattctgtgaggtctaatttttcagtatttctaagtgactttgatttta--tgaattctgctctac----------

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 14
TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtattttt-catcagctgaatttgtggtattgtgaaaactgaatttacggagctactagatgatattaattttcattgaaacatga--tatacaatccttagt---
 | || |||||| | |||||  |||||||||||||||| |||||| |||||||||| ||||| ||||| | | |   ||  || |   |      ||||    ||   ||||      ||| || |||  | | |||     ||     | |  | || |||   |      
CCTTATGCTGCAGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAGgtttgtgtgtttctactcatgctactaatttgtacggaccatattt------ctattaaatgccacttattgatgatggcttctaaactgtaaaatgtgtgagaaa

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 14
TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtattttt-catcagctgaatttgtggtattgtgaaaactgaatttacggagctactagatgatattaattttcattgaaacatgatat--acaatccttagt
 | || |||||  | |||||  |||||||||||||||| |||||| |||||||||| ||||| ||||| | | |   ||  |||   || |   ||| |    |    | | |    | |||  ||  |||||    || | ||   | || |    |       ||  
CCTTATGCTGCGGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAGgtttgtgtgtttccactgccattctttaattatctggatgctactaatattg-tac-ggacaatattttcattaaatgccccttgttgatgatggcttctaa-

upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 14
TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttcatcagctgaatttgtggtattgtgaaaactgaatttacggagctactagatgatatta--attttcattgaaacatgatatacaatccttagt-
 | || || ||| | || || ||||| |||||||||||||||||| | |||||||| ||||||||||| | | || ||  |  | |   || |  | |   |  | ||||   | |  |   |||   ||  |  | | | |    |  ||||| |  |     || | 
CCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAGgtgtgtatcttctccctattacttgtttctattttagattaatt---gcatttggaagagtgtacaaggactattaggcgatgatgatttcaagctgataatt

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), 47 (downstream exon)
Score: 289

TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttca ... aactatacagGTGAGTGCCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 330

TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttca ... aactatacagGTGAGTGCCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttca ... aactatacagGTGAGTGCCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

TCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAGgtatttttca ... aactatacagGTGAGTGCCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTA