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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactcttcattgtaatcttgtaaggtcattttgttgtttctttagattagattctgttgttttacctgtaacattttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT

Basic information

species Zea mays
transcript GRMZM2G460090_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 11
gtatgcactcttcattgtaatcttgtaaggtcattttgtt-gtttctttagattagattctgttgttttacctgtaacatt--ttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT
||  |   |||   ||| || |||| ||  ||     |||  |||  ||     |||||| | | |||     ||  |  |  ||  |||||| ||||| || |||||||||||||| ||||||||||| ||| |||| ||||| ||||||||||||||||||||||||| |||||| |||||||||||||| ||||
gtg-gtgttctatgttgaaaacttgaaatctctgacagttcattttatttctcaagattcaggtatttacttagttgctctgtttttcaaatgacagTCATGCCAGGTTGACTTGGTGAAAGATGGAGGGCATGCATACTTTATCAGGTTTCTTGACAGTTTGGATGCTTACCCAGAGCAGCGTGCAATGGCTGCTT

upper sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 12
gtatgcactcttcattgtaatcttgtaaggtcattttgtt-gtttctttagattagattctgttgttttacctgt--aacattttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT
||| |   |||   ||| || |||| ||  ||     |||  |||  ||     |||||| | | |||     ||  | |  |||  |||||| ||||| || |||||||||||||| ||||||||||| ||| |||| ||||| ||||||||||||||||||||||||| |||||| |||||||||||||| ||||
gta-gtgttctatgttgaaaacttgaaatctctgacagttcattttatttctcaagattcaggtatttacttagttgatctgtttttcaaatgacagTCATGCCAGGTTGACTTGGTGAAAGATGGAGGGCATGCATACTTTATCAGGTTTCTTGACAGTTTGGATGCTTACCCAGAGCAGCGTGCAATGGCTGCTT

upper sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
--------gtatgcactcttcattgtaatcttgtaaggtcattttgttgtttctttagattagattctgttgttttacctgtaacattttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT
        | |   |  ||||  | |||   |  ||   |  | | ||   |   |    || |  |     | |||    |   || ||     ||   |||| |||||||||||  |||| || ||||| || || | |||||| || ||||||||||||||| |||| || |  || ||||||||||||||||| || |
gttttgttgcaattatgcttc--tataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT

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: 47 (upstream exon), 48 (downstream exon)
Score: 67

CGGAATATTTCCTTATGTACTCAAACTGCTTCCAACAAATACAATAGAGTTACGTCAAATTTTAGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 66

CGGAATATTTCCTTATGTACTCAAACTGCTTCCAACAAATACAATAGAGTTACGTCAAATTTTAGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

CGGAATATTTCCTTATGTACTCAAACTGCTTCCAACAAATACAATAGAGTTACGTCAAATTTTAGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 54

CGGAATATTTCCTTATGTACTCAAACTGCTTCCAACAAATACAATAGAGTTACGTCAAATTTTAGTGTTTATATGGACAAAAATTCTCTCTCTTGATAAGgtatgcactc ... caaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctttagattagattctgttgttttacctgtaacattttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT
                               ctgtaac  putative branch site (score: 54)
                                     cattttccc  CT-rich tract
      tttagatta  TA-rich tract