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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaactgcag

Basic information

species Zea mays
transcript GRMZM2G164185_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttactt---ggaactgcag
||||||||| |||| ||||| || ||||||||||||||||||||||||||||||||| ||||||| |||||||||   | |||||||||| | ||||||  ||  ||||||| |||  ||| | || | |   |||  ||||||  |  ||||| ||||| || |||   | ||||||||
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaaga-tgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaactgcag
 | |||||  | || ||| |||| |||||||||||||||||||||||||| |||||| ||||||| ||||| |  | | |||||||     || |||| | ||||      |     ||| | |    | |  |   |    ||   |||||   ||| | ||  | |  |      
TTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAGgttagat-tcccatgtt-----tatataagtaatga------gcaatgaattcctgctgctttatcaagtcatagt--aactggctcatttttttttggccag-----

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatc-catgtgttacttggaactgcag-
 | |||||  |||| ||| |||| || || |||||||| |||||||||||||||||| |||| || ||||| |  | | |  ||||     || |||| ||||||    || || |   | |||     |    ||||  |      ||||| |   || |  |  ||| |  |||   
TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAGgttagat-tcctgtgtt-----tagataagtgatga---attatgaat--ttcat--tctactgctttgtcgagttataactggttatattttatgtttgaacatgccag

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgtt---aagagtaaataattgatgattctttgtggacaatgcataacaca-tatttttgctggagccaaactgatccatgtgttacttggaactgcag
 | |||||  | || ||| |||| |||||||||||||| |||||||||||||||||| ||||||| ||||| |  | | |||||||   | ||| ||  ||||  || | |||| |  |       ||||    | |||||  |   ||||                              
TTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagat-tcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggccag-----------------------------

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|91057148|gb|EB167566.1|EB167566
EST:     ATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT
genomic: ATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT
EST: gi|67032341|gb|CO461090.1|CO461090
EST:     ATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT
genomic: ATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT
EST: gi|71425474|gb|DR806698.1|DR806698
EST:     GGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT
genomic: GGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGT

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: 103

CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 59

CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 87

CTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG