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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattcaagttttctttttttcattgacattctcaatttgtgttaaacgccaattgcatctgttgtccactttttgtttcacaaatttggattcaaacattcgaatgaatagtttgcagggatcaaaacaattgtttcattttacttacagtgcagaaattgatagtgtgatttgtgttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG

Basic information

species Zea mays
transcript GRMZM2G117064_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
gtgagattcaagttttctttttttcatt-gacattctcaa----tttgtgttaaacgccaattgc-atctgttgtccactttttgtttcacaaatttggattca-aacattcgaatgaatagtttgcagggatcaaaacaattgtttcattttacttacagtgcagaaattgatag--tgtgatttgtgttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG
|||||||   | | ||| || ||| ||  | |||||||||     || ||||||   | | ||    | | | |||||||| |  || |    |||    |||| || |||| |||   ||  |||||              |  | |||||||     |    |  |||||| ||  | ||  ||||| | ||||||||||||||||   |||||||||||  | |||||||| |||||||| ||||||||||| ||||||||||| |  |||||||| || |||||| | || |||
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatc--taacttgca--------------tactgcattttaa----accaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG

upper sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
gtgagattcaagttttctttttttcattgacattctcaatttgtgttaaacgccaattgcatctgttgtccactttttgtttcacaaatttggattcaaacattcgaatgaatagtttgcagggatcaaaacaattgtttcattttacttacagt-gcagaaattgata-gtgtgatttgtgttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG
                                                                                       ||||      ||||| |    ||   | | | |    ||||       ||    ||| | ||| |  | |  | ||||| |    ||||  |||  | || ||| |||||||||  |||||| |||||| |||| || |  ||||||||||| |||||||| ||||||||||| |||||||||||||| |||||| | ||  | 
---------------------------------------------------------------------------------------atttaag--gaaacacttagctgg-caatgtcctacaatcatgcagtatgcaatattatccttcctcttgttgtaattgctctaagtgaactgtcat-tttcagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTT
















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|32932180|gb|CF036992.1|CF036992
EST:     GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGG                         GGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
genomic: GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
EST: gi|32930660|gb|CF035472.1|CF035472
EST:     GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGG                         GGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
genomic: GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
EST: gi|32933243|gb|CF038055.1|CF038055
EST:     GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGG                         GGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
genomic: GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
EST: gi|32931629|gb|CF036441.1|CF036441
EST:     GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGG                         GGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC
genomic: GGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 118

GAAAGGTTCGTGCAATCTTGGGAGGACGGATTCGCTTTATTCTTGCAGGTGGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

GAAAGGTTCGTGCAATCTTGGGAGGACGGATTCGCTTTATTCTTGCAGGTGGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG


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

GAAAGGTTCGTGCAATCTTGGGAGGACGGATTCGCTTTATTCTTGCAGGTGGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GAAAGGTTCGTGCAATCTTGGGAGGACGGATTCGCTTTATTCTTGCAGGTGGAGCACCTCTGTCAGGGGAAACACAGAGATTTATCAATATATGTCTTGGgtgagattca ... gttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcattttacttacagtgcagaaattgatagtgtgatttgtgttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG
       attttactta  TA-rich tract