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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtccaa--ctcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
||| | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  |||||||   | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
gta-gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtcca--actcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
    | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  ||||||  | | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
----gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
gtaagctatactcgacaacttatatattattaactttagcatttgaaattg-tacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctct--ttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                                | ||||| || |      | || || |  | | || |     | || |   |||||   |   |||||        |   |  |  ||  |  ||||| |||| ||||| |  ||  | |      | ||| |||| ||  | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
--------------------------------attttagtatgtagtggagctagttttcaagccttgacaattacttgtttgaaact-ttgtagtttagcgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
gtaagctatactcgacaacttatatat-tattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                 | || | ||| || |     |||  ||  |   |  ||    || |||| |   ||||| | || |     |    |  |      ||| ||||  |  |   |  ||||| |||| ||||| |  ||  | |     || ||| |||||||  | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
-----------------atttttgtatgtagtggagctagttttcaagccttgaca---attacttgt--ttgaaactttgtagtttagtgagtgct------aacacattgattgt---aaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                  | |     | | || |  |   ||| | ||||| | |  ||      | | |  | ||||   || | |||   | | |||    ||| ||   || || ||| |||| ||||| || || |  ||  | | |||||| |||||||||||| | |||| |||||||||||| ||||| ||||| ||||| || |||||||| ||
------------------catggccttcactaccactg--attaggaattg-attcttaag----tcatgcaatattacttaatattgctcatttgtag----actaatagttcatttgac-atatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                          ||   |  | ||     | |    ||  ||| ||   |  |||||  | |  | ||  |   | ||  | |  || ||| |   |  |  |  || ||||| ||||  | || |  ||  | | ||  || |||||||||||  | || | ||||||||||||||| || ||||| ||||||||||||||||||||
-------------------------gttccaaggtatacttagttattacgtcattggatgtttaataagtttagt-gttcatgataactgcc-tgtgatctaacac---ttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG

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|31352864|gb|CD437221.1|CD437221
EST:     ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     TGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCCAGTT                         GT-ACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGC
genomic: TGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCC-AGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGC
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     ATGATCTCACATTTCCTTCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTT                         GTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT
genomic: ATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCT

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), 49 (downstream exon)
Score: 115

GGCACCTCTTCCAAATGGTGGATGCTCTGATATGCTTGGTTGCCTGAATAATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GGCACCTCTTCCAAATGGTGGATGCTCTGATATGCTTGGTTGCCTGAATAATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GGCACCTCTTCCAAATGGTGGATGCTCTGATATGCTTGGTTGCCTGAATAATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GGCACCTCTTCCAAATGGTGGATGCTCTGATATGCTTGGTTGCCTGAATAATGATCTCACATTTCCTCCTGGAGGCTACCCATCACTGCGTTTGCCAGTTgtaagctata ... ccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
                                 tttctctttcgacc  CT-rich tract
                 tatttagt  TA-rich tract