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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatataaatgtatttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG

Basic information

species Zea mays
transcript GRMZM2G169462_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 9
gtcagtatataaatgtatttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
||||||||  | ||| | ||||   ||| |||||| | ||  ||| ||||||| | | ||  | |||||| || |||||||||||| |||||||||||||||||||| ||| ||||||| |||||||| ||||| ||||
gtcagtatgaacatgcaattgacatgttttcttttgtatgaatttccatggtagcttgaa-tttcctgtggaatatagGTTGTCGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAACAGGTCATAACTCCAACTG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 9
gtcagtatataaatgtatttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
||||||||  ||||| | ||||   ||| |||||| | || |||  ||||||| | | ||  |  ||||| || ||||||||| || |||||||||||||||||||| ||| |||||||||||||||| ||||| ||||
gtcagtatgaaaatgcaattgacatgttttcttttgtatgagttcccatggtagcttgaattttgctgtggaatatagGTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------gtcagtatataaatgt---atttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaa-atagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
                             ||| |  |||| |     | ||| |      | | || | |  | |||  |  | |  |  |   || |||      | ||||||| |||||||| || ||||||||||| |||   ||||||||||| |||||||| ||||
gtgggtattatttcctagagccacttggttcatttgataacttcttgacttggtagtgggtttcttttatttggttgattcat-ttatctagtcccttgtatctttacagGTTGTTGAACATGGCCTAGGTCATCTTCCATTCACAGAAAAGCAGGTGATCACTCCAACTG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ31180 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtatataaatgtatttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
                             | | |    | |    | |||     |      || |          |||| |||||||||||||| |||||||| || ||||||||||| || || || ||||| || |
----------------------------gtatgtgtcattgacacgaatgacgctgatgttttctcctc------cagGTCGTCGAACATGGTCTGGGTCATCTCCCATTCCAGGAAAAACAAGTGATTACTCCAACAG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ17251 (Selaginella moellendorffii), 3'ss of exon 7
gtcagtatataaatgtatttgatgagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
                             | | |    | |    | |||     |      || |          |||| |||||||||||||| |||||||| || ||||||||||| || || || ||||| || |
----------------------------gtatgtgtcattgacacgaatgacgctgatgttttctcctc------cagGTGGTCGAACATGGTCTGGGTCATCTCCCATTCCAGGAAAAACAAGTGATTACTCCAACAG

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|94473336|gb|EB702294.1|EB702294
EST:     CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTG                         GTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC
genomic: CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC
EST: gi|5915469|gb|AW053110.1|AW053110
EST:     CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTG                         GTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC
genomic: CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC
EST: gi|24765651|gb|CA400810.1|CA400810
EST:     CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTG                         GTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC
genomic: CCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATC

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), 46 (downstream exon)
Score: 69

ATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

ATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

ATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 182

ATACGAGGCATGCACACAATAATAAGGGATGCTGCCACAGCAACACATGATTTCATATTTTATGCTGATCGGTTGATTCGATTGgtcagtatat ... tgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttatcttttatgtgggtttgcatggtatcgtaaaactccctgtgaaaaatagGTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTG
                                      ctccctgt  CT-rich tract
     atcttttat  TA-rich tract