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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgtctccaccatttcatcactatactgaattctatagcacggttgtaaatgttatctttgaggctgtcataattcttattggtagtcattctt...

Basic information

species Zea mays
transcript AC182617.3_FGT001
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC182617.3_FGT001 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 5'ss of exon 2
CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgtctccaccatttcatcactatactgaattctata-gcacggttgtaaatgttatctttgaggctgtcataattc-ttattggtagtcattctt
||||||| | |||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| ||||||||||| || ||||| || || |||||| |    ||     ||||||  || |       |    ||     ||| |||   |||| |  |     | ||  | |||| | | |  ||       | 
CTTCGGCGTCGGCGCCGACGGTGTGATCTTCGTCATGCCGGGGGTCAATGGCGCGGACTACACCATGAGGATCTTCAACTCGGACGGCAGTGAGCCGGAGgtgagca-atccattgcatttctgcagtgcgtgataggaaatgtattcgggtgttggtgtt-ttgtgatatccgtagtgattcgtcaatcataaatgcaatg

upper sequence: AC182617.3_FGT001 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 2
CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgt--gtctccac---catttcatcactatactgaattctatagcacggttgtaaatgttatctttgaggctgtcataattcttattggtagtcattctt
||| || ||||| || |||||||| ||||||| |||||||||| |||||||  | || || || ||||| || ||||| ||||||||||| || || |||||   |     | |||||   ||| |  ||  |  | || ||  |  ||   | ||||  | ||   | |  |   |      |    | | |  ||| |||   
CTTTGGGATTGGTGCTGACGGTGTGATCTTCGCCATGCCGGGGATCAATGGCACTGATTATACAATGAGGATTTTCAATTCTGATGGCAGTGAGCCTGAGgtaattaacaatttccacgtacatgttttctgttgagtggatcgt-cagtctgtttgttga-gtagccctgaaaatttgagctaaaaatgtggaaagtaatt---
















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|149103897|gb|EE289312.2|EE289312
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|148932662|gb|EC876592.2|EC876592
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|149014406|gb|EE044007.2|EE044007
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|74235623|gb|DT643537.1|DT643537
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|71757461|gb|DR955398.1|DR955398
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|148930368|gb|EE284809.2|EE284809
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|71432546|gb|DR813596.1|DR813596
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
EST: gi|50325885|gb|CO521011.1|CO521011
EST:     GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA
genomic: GTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAA

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: 281

CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAAAATCTGCAGGGGACAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAAAATCTGCAGGGGACAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAAAATCTGCAGGGGACAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

CTTCGGCATTGGCGCCGACGGTGTTATCTTCGTCATGCCGGGGGTCAATGGTGCCGACTACACCATGAGAATCTTCAACTCTGATGGCAGCGAACCAGAGgtgcgtgtgt ... tgtttttcagATGTGTGGTAATGGAGTCCGTTGCTTCGCTCGGTTTATAGCCGAGATTGAAAATCTGCAGGGGACAAATAG