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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttcacaaggaccaattcagatactttgcagtgactacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

Basic information

species Zea mays
transcript GRMZM2G048150_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
gtatgcttca-caaggaccaattcagatactttgcagtgactacaa--tatatctatgc-taatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT
||||| ||   |||  |  |||  ||| |  |  ||    ||| |   |||||| | || || || ||||||||  |  |||  ||||  | ||||| ||||||||||||||  ||||||| ||||||||| |||| ||||||||| || | ||||||||||| |||||||| ||||| |||||||| || || |||
gtatgttttttcaacaattaatctagacatatcacaagagctaaagattatatccaagcctattaacctgttttatc--cctcttttgatt-tgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT

upper sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 2
gtatgcttcacaaggaccaattcagatactttgcagtgactacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT
           || || |||  |   |   |||   ||| || | | ||||     |  |    || ||   |       ||||  ||||||| ||||||||||| ||| ||||||| || |||||| | || |||||||||||||| |||||||||||||| || || ||| | ||  | |  || ||| | 
---------gtaatgaacaaaactact-tattgagatgattaaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATA

upper sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
gtatgcttcacaa-ggaccaattcagatactttgcagtgactacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT
           || |||| ||   |  ||  |||   ||| || | | ||||     |  |    || ||   |       ||||  ||||||| ||||||||||| ||| ||||||| || |||||| | || |||||||||||||| |||||||||||||| || || ||| | ||  | |  || ||  | 
---------gtaatggacaaaactactta--ttgagatgatta-attttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA

upper sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 2
---gtatgcttcacaaggaccaattcagatactttgcagtgactacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT
    |||||||  | | | |  | | | || ||      | |||    | |   |||  |     |     |||   |   | ||||    |||||||| |||||||| ||| |||| || ||||| ||  | || |||||||||||||| || ||||||||||| ||||| ||| | |||| |   || ||  | 
gtaatatgcttacctatgccttaat-atattctagatgtttactcattttttattattttccagcctaacattga--gttgattttgaaattgcagTGTTGTTCTTTTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148985819|gb|EE029780.2|EE029780
EST:     TGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG                         TGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTAT
genomic: TGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATGgtatgcttca ... gtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTAT




















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: 48 (upstream exon), 48 (downstream exon)
Score: 60

GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATGgtatgcttca ... gtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT


Block sizes: 36 (upstream exon), 45 (downstream exon)
Score: 23

GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATGgtatgcttca ... gtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 29

GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATGgtatgcttca ... gtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATGgtatgcttca ... gtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT
               tgctaat  putative branch site (score: 54)
                                     cctactttgtctct  putative PPT
     aatatatctat  TA-rich tract