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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatgtcatatgtgtaaagtgaatttgttggtgggctctagttcactaatttgttgtatttactaatgtaccgttgcttacagcttgttatcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG

Basic information

species Zea mays
transcript GRMZM2G160842_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 3'ss of exon 2
tatatgtcatatgtgtaaagtgaatttgttggtgggctctagttcactaatttgttgtatttactaatgtaccg-ttgcttacagcttgttatcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG
||  |  |  | | ||    | |  | | |     |   | || |   | ||| ||| | |   ||||  |  | || ||| || | |  | ||||  ||||| ||||||||||||| ||||| |||||||||||  | ||||| ||||| ||||||
tagctagctgacg-gtgggattagatggattacttgtgatggtccttgactttcttggagtaggtaattcattgctttcttgcaaccttctgtcttcctagGTTGCTTGGGCATTGTTGATGGAGATGATGTTGAGCTTAATAACCTTCACCGACAG
















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|211107289|gb|FL028196.1|FL028196
EST:     TGGAGGTTTGGGCTCTCCCCTGACATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|211108194|gb|FL028200.1|FL028200
EST:     TGGAGGTTTGGGCTCTCCCCTGACATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|37423894|gb|CF649677.1|CF649677
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCC                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|149009441|gb|EE041457.2|EE041457
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCCGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCCTC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|211107292|gb|FL028199.1|FL028199
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTYGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|211108195|gb|FL028201.1|FL028201
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATG
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATG
EST: gi|148954835|gb|EC900308.2|EC900308
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
EST: gi|89761475|gb|DY689476.1|DY689476
EST:     TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTTGA-TAATCCTCAT
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATT-GAATAATCTTCAT
EST: gi|211107291|gb|FL028198.1|FL028198
EST:     TGGAGGTTTGGGCTCTCCCCTGACATTGTATCTAGCAGCTTGTGGTGTCG                         GTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC
genomic: TGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATC

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: 399

GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 182

GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 265

GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 276

GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCGgtaattttct ... atcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaatttgttgtatttactaatgtaccgttgcttacagcttgttatcttattagGTCGCTTGGGCATTGTGGATGGTGATGATGTTGAATTGAATAATCTTCATCGACAG
                                           ttatctt  CT-rich tract
         ttgtatttactaat  TA-rich tract