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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtctatgctacctcatcagtcttattttgtgctatgtcctaatgagtttagtctcctgtattttttgttaccgccttttaagcactagaccaataactatactttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC

Basic information

species Zea mays
transcript AC208418.3_FGT009
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208418.3_FGT009 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 7
gtgtctatgctacctcatcagtcttattttgtgctatgtcctaatgagtttagtctcctgtattttttgttaccgccttttaagcactagaccaataactatactttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC
|| || || ||| | ||      ||||    || | | || ||           | |||  |||| |||| |||  |||  ||  |||| |      || ||  |||  |||||||||||||||||| |||||||||||||||| || ||||||||||||||||||||||||  |||||| ||||||||||| |||||||||||||| |||||||
gtttccatcctagcccaa-----ttatccaatgttgtttctta-----------ccccttgatttgttgtaaccatcttagaaatactaaa-----gaccatcttttaaatgcagATGATGTGGAGGCTAAATTTCTTTGTGGCCTTCTGTTGCATTGTCCTTGACAATGATTACATGCTGTATTATATATGTCCAATGCACACACTTTTTACTC

upper sequence: AC208418.3_FGT009 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 8
gtgtctatgctacctcatcagtcttattttgtgctatgtcctaatgagtttagtctcctgtattttttgttaccgccttttaagcactagaccaa--taactatactttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC
||     |  |    | | | |   ||||||   ||  |  || |   ||   | |||| |   | ||  |         ||| || || ||| |  |   || | ||||  |||||||||||||| || | ||||| |||||||| || ||||| ||||| ||| |||||||    |||||||| |||||||||||||||||||| || || ||| 
gtaagagtcattgaccttaaataccattttgctttacttggta-tccattgtctatccttttcctattactctttttgcataaacaatatacctaactcgttaaaatttct-tgcagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: AC208418.3_FGT009 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 8
------gtgtctatgctacctcatcagtcttattttgtgctatgtcctaatgagtttagtctcctgtattttttgttaccgccttt---taagcactagacc-aataactatactttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC
      | |||  ||  |||| |  | |   ||||| |||| |  | |  ||      ||||    | |||  ||||||    |||   ||| || || ||| ||    |  |  |||| |||||||||||||| || | ||||| |||||||| || ||||| ||||| ||| |||||||    |||||||| |||||||||||||||||||| || || ||| 
gtaatagagtccttg--acctta--aataccatttt-tgcttta-ctttgtgtccactgtctatcct-tttcctgttactctttttgcataaacaatatacctaactcgttaaaattccttgcagATGATGTGGCGGCTTAATTTTTTTGTGGCCTTCTGTTGTATTGTGCTTAACAATGACTATATGCTCTACTATATATGCCCAATGCACACGCTTTTCACTT

upper sequence: AC208418.3_FGT009 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 2
gtgtctatgctacctc--atcagtcttattttgtgctatgtcctaatgagtttagtctcctgtattttttgttaccgccttttaagcact--agaccaataactatactttcca-tgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC
||| |  || ||  ||  | | || | ||  | |      |   | |||  ||  ||   |  ||||| | |       |||| |  | |   ||     | || ||||||| | |||||||||||||| || |||||||||||||||||||||| |||||||| ||| |||||||   |||||| || ||||| ||||| |||||||| || || ||||
gtgaccttgttaattctgaactgtttcatcatttctctattagaagtgatattgttccttttcattttctatatttcaattttgataatttaggatgtgaatctttactttctaatgcagATGATGTGGCGGCTAAATTTCTTTGTGGCATTTTGCTGCATTGTTCTTAACAATGACTACATGCTATACTATATCTGCCCCATGCACACGCTTTTCACTC

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), 27 (downstream exon)
Score: 27

AATCTGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATTTCTCCTATTACTATATCAAGAAAGATTTTAGTATTGCAAGATTTGCTCAGgtgtctatgc ... ttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC


Block sizes: 47 (upstream exon), 27 (downstream exon)
Score: 38

AATCTGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATTTCTCCTATTACTATATCAAGAAAGATTTTAGTATTGCAAGATTTGCTCAGgtgtctatgc ... ttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 40

AATCTGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATTTCTCCTATTACTATATCAAGAAAGATTTTAGTATTGCAAGATTTGCTCAGgtgtctatgc ... ttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC


Block sizes: 49 (upstream exon), 20 (downstream exon)
Score: 108

AATCTGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATTTCTCCTATTACTATATCAAGAAAGATTTTAGTATTGCAAGATTTGCTCAGgtgtctatgc ... ttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttttgttaccgccttttaagcactagaccaataactatactttccatgcagATGATGTGGAGGTTAAATTTCTTTGTGGCATTTTGTTGCATTGTCCTTGACAATGATCTCATGCTCTATTATATATGCCCAATGCACACACTATTTACTC
                                caataac  putative branch site (score: 108)
                                         tactttcc  putative PPT
                                 aataactatacttt  TA-rich tract