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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacaatttctatggcataaacttctgaagttttgaaaaatcgtttttggtatcactgaaagttgttgtttttttcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA

Basic information

species Zea mays
transcript GRMZM2G089159_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
gtatgcacaatt--tctatggcataaacttctg----aagttttg--------aaaaatcgtttttggtatcactgaaagttgttgtttttttcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA
|||||||||| |  || ||  | |||| |  ||    || ||  |        ||||||      | |||| | |     |   |  ||| |   | |||||| |  ||||| ||||||||||||||||||||| | ||||| ||||||||| | |||||||| ||||| ||||||||||| || |||||||||||||||||
gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA

upper sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 3
-gtatgcacaatttctatggcataaacttctgaagttttgaaaaatcgt--ttttggtatcactgaaag-------ttgttgtttttttcatatg--cagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA
  | |    | | |  ||    | |  |||||   ||||      || |  |||    || |   |||         |     |   ||| | |    ||| ||  |  | || ||||| || || |||||| ||||| ||||||||||| | |||||||| | |||||||||||| || ||||| |||| |||||| ||
tttctttttagtcttgataatttcatattctgttttttttttttctcatactttctacataagaaaaaaaaccaaactaacaatccattcctctaaatagGTCGAATTAGAAATATCTACTTCCCATTTGACATTGAGACTGATACCGCATTGAGTGTTGCAAATGAAATGGTAGCTGAGCTCGACATAAATGACCAAGA

upper sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtatgc-acaatttc-tatggcataaacttctgaagttttgaaaaatcgtttttggtatc---actgaaagttgttgtttttttcatatg--cagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA
                                         || |   | |||||| |||    |    ||    |   |||  | ||          | |   ||| | | |   |   | |   || |    ||| ||  |  | |||||||| || || |||||| ||||| ||||||||||||| |||||||| | |||||||||||| || || ||||||| |||||| ||
gttagcatttcactttcttattttcttcttgaacttttttagtctttgataatttcatattctgttgtttttctgatacttgctacataagcaaaaaaaaccaaactaacaatgcattcctctaaaatctaaatagGTCGAATTAGAAACATCTACTTCCCATTTGACATTGAGACTGATACCGCACTGAGTGTTGCAAATGAAATGGTAGCTGAGCTTGATATAAATGACCAAGA

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: 305

AATGAAGGTGAGCTTCTTGGCAATGTGGATATAACAATCAAAGGGAGAAAGAGTGAGGATGGAGGCATATTCCTTAGATTGCGGATTTCTGATGATGATGgtatgcacaa ... tcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

AATGAAGGTGAGCTTCTTGGCAATGTGGATATAACAATCAAAGGGAGAAAGAGTGAGGATGGAGGCATATTCCTTAGATTGCGGATTTCTGATGATGATGgtatgcacaa ... tcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

AATGAAGGTGAGCTTCTTGGCAATGTGGATATAACAATCAAAGGGAGAAAGAGTGAGGATGGAGGCATATTCCTTAGATTGCGGATTTCTGATGATGATGgtatgcacaa ... tcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

AATGAAGGTGAGCTTCTTGGCAATGTGGATATAACAATCAAAGGGAGAAAGAGTGAGGATGGAGGCATATTCCTTAGATTGCGGATTTCTGATGATGATGgtatgcacaa ... tcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgaaaaatcgtttttggtatcactgaaagttgttgtttttttcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA
                                 ttgttgtttttttc  CT-rich tract
                                    ttgtttttttcatat  TA-rich tract