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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaactaatcgtgttttattgtcacatcctccatcttcttccatagcacatgttaccttactgacacttcaattttaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG

Basic information

species Zea mays
transcript GRMZM2G100809_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 6
gtacaactaatcgtgttttattgtcacatcctccatcttcttccatagcacatgttaccttactgacacttcaattttaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG
              ||     |      | | | | | ||| | || | |     |     |   |   |   | |  ||||||||| |   | | | |||  | ||||||||| |||||| ||||||| ||||||||||||||||||||||| || || ||||||||||||||||| || ||||||||||||||||||||
--------------gtaaagctaaagtgtacccaaccgtctac-attgtatgaaatgtgccatgaatgttgacactcaaaactaataggtgttctgtgctttgacagGTGTTATTATCTGGTTGCTTGCTATTATCTACTTCATATCTGGTGTACCTGGTGCTTATGTGTTATGGTACCGCCCTCTTTATAATGCAATGAG

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G11180.2 (Arabidopsis thaliana), 3'ss of exon 6
gtacaactaatcgtgttttattgtcacatcctccatcttcttccatagca---catgttacct-tactgacacttcaattttaaacta--------atatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG
      ||  |  |||| | ||  |||||      | ||| |   ||||    || ||   || |  ||   | ||  | || |  ||        || |    | |||  ||    ||| || |  || ||||| || ||| |||| ||||||||||| ||||| || || |  ||||||||||||||||||||||| ||   |||  | ||
----gtctctttttgttctctta-cacatgtcttgtgttcctttttagctggccaagtcttctgtgatggtccgtctctgtttatttacagtcttgattttttttttctcttttttcagGAGTAACAATTTGGCTTCTCGCCGTTATTTACTTCATATCGGGTGTTCCAGGAGGCTATGTGTTATGGTATCGGCCTCTCTACCGTGCCTTCAG

upper sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
gtacaactaatcgtgttttattgtcacatcctccatcttcttccatagcacatgttaccttactgacacttcaattttaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG
       || |   |   | |  |||| |||   | |||     |||     ||| ||||| |  | | ||   | || || |    |  | | |          ||||   |  || ||| | |||||||| ||||||||| |||| || || || || ||||||||||| |||||||| |||||||||  ||| |||||
-----gttagtttggaactttgttcacctcccaaaccttggggaatat----tgtaaccttcc--ataattgggtcttgaatttgctttccttgt----------agGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG

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: 347

GATTGATAGCGTGCCTCTTTTGGAATATCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtacaactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GATTGATAGCGTGCCTCTTTTGGAATATCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtacaactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 192

GATTGATAGCGTGCCTCTTTTGGAATATCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtacaactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

GATTGATAGCGTGCCTCTTTTGGAATATCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtacaactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaccttactgacacttcaattttaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG
                                          tctacttc  CT-rich tract
               acttcaattttaaact  TA-rich tract