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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgtttgtgtttgcatttactcccatcatagcgatttttatgcagtctttgtggtaattcttgtgtttttag

Basic information

species Zea mays
transcript GRMZM2G175867_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175867_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g08930.1 (Oryza sativa), 5'ss of exon 7
AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgtt-------tgtgtt--tgcatttactcccatcatagcgatt-tttatgcagtctttgtggtaattcttgtgtttttag------------------------
||| |||||||| |||||| | || |||||||| || |||||| ||||||| ||| ||||||||||||||||||||||||||||||||||||| || |||||| |||||       ||||||  |   ||| |     |  |    ||  ||| | |   |     || || |  | ||  |||                          
AGAAGGGGATTGCCCAACACTGGTCTGCACTGACCTAGCAGCTCGAGGCCTAGACTTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCAAACTCTgtacgtgttgacttcttgtgttatttttttttcctttgttctgttcatcatttttcccacccccagggaaactgatatgcatttttttcttgtatatttttcctttttag

upper sequence: GRMZM2G175867_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0001g02530.t01 (Vitis vinifera), 5'ss of exon 7
AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgtttgtgtttg--catttactcccatcatagcgatttttatgcagtctttgtggtaattcttgtgtttttag--------------------------------
||| || ||||| || ||||| |||||||| ||| |||| ||||| ||  ||||  |||||||||| ||||||||||||||||| || || | |||||||||| |  |   | ||||   | ||  |    |   ||    | || ||   | ||      | ||      | ||| |                                
AGATGGAGATTGCCCCACATTGGTATGCACGGATTTGGCTGCTAGGGGATTGGATTTGGATGTTGATCATGTCATCATGTTTGATTTTCCCTTGAATTCTgtaagcatcattctttgactacttgttgaggtttgagaagatcttctgtt-ttttcactcaactttcctcatatttggaaactaaactctgtttttctttgaccttttag
















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|67038766|gb|CO465021.1|CO465021
EST:     TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCT                         ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCCAAG
genomic: TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
EST: gi|148986358|gb|EE030095.2|EE030095
EST:     -GACCCTGGATGTGGACCATGTCATCATGTTTGACTTCCCATCGAATTCT                         ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
genomic: GGA-CCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
EST: gi|33942668|gb|CF349268.1|CF349268
EST:     TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCT                         ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCCAAG
genomic: TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
EST: gi|6827364|gb|AW331007.1|AW331007
EST:     TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCT                         ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
genomic: TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
EST: gi|78123116|gb|DV541500.1|DV541500
EST:     TGGACCTGGATGTTGACCATGTCATCATGTTTGACTCCCCATCGAATTCT                         ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG
genomic: TGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG

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), 48 (downstream exon)
Score: 116

AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 54

AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

AGAGGGGGATTGTCCAACATTAGTATGCACTGATCTGGCAGCTAGAGGCCTGGACCTGGATGTTGACCATGTCATCATGTTTGACTTCCCATCGAATTCTgtatgtgttt ... gtgtttttagATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG