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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcacaagtcatctatttttagtttatcatagttttatcgttgtcatgaaagaaacattccttttttaattgtattatttttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG

Basic information

species Zea mays
transcript GRMZM2G068212_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 13
gtaaaatcacaagtcatctatttttagtttatcatagttttatcgttgtcatgaaagaaacattcc----ttttttaattgtattatttttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG------------------------------------------------
          ||||  |  |||| | | | || |  |   | | | |   ||   | |||  |||     | |||| || |||  || || |||  ||||| | |||||||||||||||||| || ||||||||||||||||| ||||| |                                                
--------gtaagt-gtaaatttattgctgattactgacatgtggataagatacca-aaatgttctgaattcttttgatggtaacatcttccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCGGTGAGTAATTATGCTATACTAGACCTGAGGGTACTCACACTTTAATAG

upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os09g06499.1 (Oryza sativa), 3'ss of exon 13
gtaaaatcacaagtcatctatttttagtttatcatagttttatcgttgtcatgaaagaaacattcc----ttttttaattgtattatttttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG
          ||||  |  |||| | | | || |  |   | | | |   ||   | |||  |||     | |||| || |||  || || |||  ||||| | |||||||||||||||||| || ||||||||||||||||| ||||| |
--------gtaagt-gtaaatttattgctgattactgacatgtggataagatacca-aaatgttctgaattcttttgatggtaacatcttccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCG

upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 12
gtaaaatcacaag--tcatctatttttagtttatcatagttttatcgttgtcatgaaagaaacattccttttttaattgtattatttttct----ttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG
 ||| || | | |  |    | | ||     |   | |||| |  | ||  |||     ||  | ||  ||||| ||| ||| |  ||| |    || |||||||   | ||| | || ||||| |||||||||||||||||||||||||| |
-taatataaaatgattttcttgtgttggacatgcaaaagttgtggcatttccatatgctaagtaatcactttttcattttataaggtttttgaaattgtagGTTGGGGTTTCACTTGCTTTTGTCATTCATGAGTCAGCAAATCCACATATTG

upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 12
gtaaaatcacaagtcatctatttttagtttatcatagttttatcgttgtc---atgaaagaaacattccttttttaattgtattatttttct----ttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG-
   |||  |  | |    | | || |   |   | |||| |  | || ||   |||  |  |  ||  ||||| | | | ||| |  ||| |    || |||||||   | ||| | || ||||| |||||||||||||||||||||||||| | 
---aaaaaatgattttcttgtattcaacatgcaaaagttgtggcattttccatatgctaagataatcacttttctcactttataaggtttttgaaattgtaggTTGGGGTTTCACTTGCGTTTGTCATTCATGAGTCAGCAAATCCACATATTGG

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), 46 (downstream exon)
Score: 32

CATCTTCTTGTGGGCTATTGATAAGAAAGATTTCTTTTTATGGGCAATCACATTTATCACAACATTAGTTTTTGGCATTGAGATTGGCGTCCTTGTTGGGgtaaaatcac ... ttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CATCTTCTTGTGGGCTATTGATAAGAAAGATTTCTTTTTATGGGCAATCACATTTATCACAACATTAGTTTTTGGCATTGAGATTGGCGTCCTTGTTGGGgtaaaatcac ... ttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 141

CATCTTCTTGTGGGCTATTGATAAGAAAGATTTCTTTTTATGGGCAATCACATTTATCACAACATTAGTTTTTGGCATTGAGATTGGCGTCCTTGTTGGGgtaaaatcac ... ttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 103

CATCTTCTTGTGGGCTATTGATAAGAAAGATTTCTTTTTATGGGCAATCACATTTATCACAACATTAGTTTTTGGCATTGAGATTGGCGTCCTTGTTGGGgtaaaatcac ... ttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgttgtcatgaaagaaacattccttttttaattgtattatttttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG
                            ttttaat  putative branch site (score: 103)
                                     tattatttttcttttt  putative PPT
                 aaacattcctttttta  TA-rich tract