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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagcacactccgcttattgttccatatctctaccagtacaactaaactgagtaaagtttgggtgtgttgatcattcacatgataattgtatcactatactcagttgatcttttctcttatcaagattcttcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG

Basic information

species Zea mays
transcript GRMZM2G165692_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 3'ss of exon 3
gttgagcacactccgcttattgttccatatctctaccagtacaactaaactgagtaaagtttgggtgtgttgatcattcacatgataattgtatcactatactcagttgatcttt-tctcttatcaagattcttcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG
||||| ||  || | || |||||| |  | || || |   |    ||||     ||||| |  | ||  |   |  |   ||| |||||| |||  || |  | | ||||  ||| |||||||||| ||   |||||| ||||   | |||||||||||||||||||||||||||||||||||||||| || ||| |||| || ||||| |||||||| || ||||||||||||||||| |||||||||||||
gttgatcatgctgcactaattgtttcgaagctatatcttcat---taaatattataaagctgagttgaatgtgt--tcagcattataattctatatcttttgttatttgaagtttgtctcttatcaggaccattcatgatttt---aatgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCAGCTGGGGAACCAGAAGAAACAAAATCCTTGCTGCCTGCTCTACCATTGCTTATTGCTCACCTTG

upper sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
-------------------gttgagcacactccgcttattgttccatatctctaccagtacaactaaactgagtaaagtttgggtgtgttgatcatt-cacatgataattgtatcactatactcagttgatcttttctct-tatcaagattcttcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG
                    ||||      | |  | | |  |    || | |       |||      |||| || |      | |||  ||| ||   || ||||||       |  || |  |  ||  ||||||   |    | ||| |        | |    |||||||||| |||||||||||||| || ||||| || || |||||||| || || ||||| ||| | ||  | |||||  | || ||||| |||||||| ||||
gtctgaagtttcatcttcctttgaatgatgttcaatgacttgtatgaatgtttgtactctcaaaaggcttgagcaa-gcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttacattttgtggtgaatgtcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG

upper sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g02290.t01 (Vitis vinifera), 3'ss of exon 3
gttgagcacactccgcttattgttccatatctctaccagtacaactaaactgagtaaagtttgggtgtgttgatcattcacatgataattgtatcactatactcagttgatcttttctcttatcaagattct--tcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG
                                                  ||  | |    ||  ||| ||     || | ||    || | |  |||| |   |     |||  | | ||||||  ||| |  | |   || ||  |||||||||||| ||||||||||||||||||||||| || || || || ||||| || ||||| ||| | ||  | |||||  ||||| |||| ||||||||  | |
--------------------------------------------------tggatta---ctgtttgtcttaccatttaaaattggcatgggagaactaaaagaaaactttctgat-tattatcacaattataattacaattgttatattgcagTTGCTTGAGGCAGCTTGGTGCCTTACAAATATTGCAGCTGGAAAACCAGAAGAAACAAAAGCTTTGGTGCCTGCATTACCACTGCTTATTGCTCATTTGG

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|31354240|gb|CD438597.1|CD438597
EST:     CAGTCCCTCTACTAGTGCAGTCTCTGTCGTTCGGATCACCAGATGAACAA                         TTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
genomic: CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
EST: gi|71442874|gb|DR823924.1|DR823924
EST:     CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAA                         TTGCTAGAGGCAGCTTGGTTGCCT-ACAAACATAGCGGCAGGGAAACCTGA
genomic: CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGT-GCCTTACAAACATAGCGGCAGGGAAACCTGA
EST: gi|78080888|gb|DV509300.1|DV509300
EST:     CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAA                         TTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
genomic: CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
EST: gi|148969108|gb|EE019843.2|EE019843
EST:     CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAA                         TTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
genomic: CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
EST: gi|71442875|gb|DR823925.1|DR823925
EST:     CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAA                         TTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG
genomic: CAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAG

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: 43 (upstream exon), 39 (downstream exon)
Score: 12

GTTGTCCCAGTCTGAAGTACCTCCAGTTGATGCAGCAATTAAAGCTGGAGCAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG


Block sizes: 41 (upstream exon), 39 (downstream exon)
Score: 34

GTTGTCCCAGTCTGAAGTACCTCCAGTTGATGCAGCAATTAAAGCTGGAGCAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 29

GTTGTCCCAGTCTGAAGTACCTCCAGTTGATGCAGCAATTAAAGCTGGAGCAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG


Block sizes: 20 (upstream exon), 39 (downstream exon)
Score: 4

GTTGTCCCAGTCTGAAGTACCTCCAGTTGATGCAGCAATTAAAGCTGGAGCAGTCCCTCTATTAGTGCAGTCTCTGTCATTTGGATCGCCAGATGAACAAgttgagcaca ... ttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactcagttgatcttttctcttatcaagattcttcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG
                                           ttttaat  putative branch site (score: 4)
                               ttcttcatgctttttt  CT-rich tract
                                     atgcttttttaatt  TA-rich tract