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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttcttgtcttctattgtttttctgatgttctgtatattgttgtctatggtagttgcagttcagcaaagatgtgtattactaaccctgctttatgtccaaatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG

Basic information

species Zea mays
transcript GRMZM2G121851_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121851_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g32160.2 (Oryza sativa), 3'ss of exon 5
gtattgttcttgtcttctattgtttttctgatgttctgtatattgttgtctatggtagttgcagttcagcaaag-atgtgtattactaaccctgctttatgtccaaatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG
             | | | |  | |||||    || ||  |    ||||  ||| |||| || ||||||||||   |||| ||   | |||     |||||  |||||  |||||||||| ||  ||||||||||||||||||||||||||| ||| || || ||| ||||||| ||| ||||  ||||||| ||||||   |||||||| ||  
----------aagcatatgtcatatttctatctttttgcctgaatttgtagatgatagtggccgttcagcaaaatgtgtggatatgtgacc-----ttatgctcaaattatgcagATATTGGGCAGTGGCATGTCAACAAAGATGTGGGAGGTCACAGTTGAGCATTCAAAAACCTGTATTCTCCCTGACAAGGTGCATTTGTACTATCCAGACA

upper sequence: GRMZM2G121851_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g60890.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------gtattgttcttgtcttctattgtttttctgatgttctgtatattgttgtctatggtagttgcagttcagcaaag-atgtgtat-tactaaccctgctttatgtccaaatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG
                                                   ||| ||     | |   |||||||   ||   |   | ||  | |||   ||| |||| ||  |||||||||  || || || || |  ||||   ||||   |||| | |||||||||| ||  |||| ||||||||||||||||||||||                                                               
tctgagctcaaaagttttttcctcagcaagcagatgtcacatttctatccatat-gtctgaatttgtcattgtttaattgtgttgtagcatgcttttgcagATGATAGT-GCTATTCAGCAAAATATATGGATATATTGGCCCT--CTTATTCTCAAACCATGCAGATATTGGGCAGTGGTATGTCAACAAAGATGTGGGAGGT--------------------------------------------------------------

upper sequence: GRMZM2G121851_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 5
gtattgttcttgtcttctattgtttttctgatgttctgtatattgttgtctatggtagttgcagttcagcaaagatgtgtattactaaccctgcttt-atgtccaaatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG
   || |   |   ||      |  || | |||| ||| | |    ||    |     || ||            | || | || ||||  || ||  ||||        |||||||  | ||    || |||||||| ||||||||||| | |||||||||||||||    || |||||  |   | | |   |   |   |||| ||||  ||
--gttctgactactttaggcaatagttttcatgt-ctgcaaaagaatgaacct-----tttcaccctccttggtctatgaagtaataacaatgtttggatgtt-------tgcagATCCTTGGCACAGGTATGTCAACTAAGATGTGGGAAGTCACTGTGGAACATGCTCGGACGTGTGTAATTGATAAGAGGATTTTTATGTACTGTCCTCCTG

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|71332862|gb|DR803444.1|DR803444
EST:     TCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAG                         ATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACAT
genomic: TCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACAT
EST: gi|211211397|gb|FL246856.1|FL246856
EST:     TCAAAGATTATCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAG                         ATATTAGGTAGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACAT
genomic: TCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACAT

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

CAAGGAAGGTGCTTTTCACAAGCGTTTGAATAGGGAGAACATTTGCACTGTCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

CAAGGAAGGTGCTTTTCACAAGCGTTTGAATAGGGAGAACATTTGCACTGTCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

CAAGGAAGGTGCTTTTCACAAGCGTTTGAATAGGGAGAACATTTGCACTGTCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 77

CAAGGAAGGTGCTTTTCACAAGCGTTTGAATAGGGAGAACATTTGCACTGTCAAAGATTTTCTCACCTTGTTAAATCTTGATGCTTCTAGGCTTCGAAAGgtattgttct ... aatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagttcagcaaagatgtgtattactaaccctgctttatgtccaaatcgtgcagATATTAGGTGGTGGCATGTCAACAAAGATGTGGGAGGCCACTGTGGAACATGCAAAAACATGTGTTCTAACTGACAAAGTGCATCACTACTATCCTGATG
                       tactaac  putative branch site (score: 77)
                    tattactaa  TA-rich tract