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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcag

Basic information

species Zea mays
transcript GRMZM2G142334_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactc---aaaactgcag
||||||||| |||| ||||| |||||||| ||||||||||||||||||||||||||| ||||||| |||||||||   | ||||||||||| ||||||  ||  ||||||| | |  ||||| |  | |   |||  |||||  ||  ||||| ||||| || ||     |||||||||
CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcag

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttc-tttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcag
 | |||||  | || ||| |||||||||| |||||||||||||||||||| |||||| ||||||| ||||| |  | | ||||||| | |||| ||||      |   ||  |||    | |  |   |||| |    ||||  ||    |  |      |                
TTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAGgttagat-tcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagta--actggctcatttttttttggccag----------------

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcag
 | |||||  |||| ||| |||| || || |||||||| |||||||||||||||||| |||| || ||||| |  | | |  |||| |||||| | ||  ||  |   ||     | |    |    |   || |  ||||   | |  | ||   ||       ||         
TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAGgttagat-tcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggt-tatattttatgtttgaacatgccag--------

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 10
CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttcttccatgttaagataaataattgatggttctttgtgca-caatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcag
 | |||||  | || ||| |||||||||| |||||||| |||||||||||||||||| ||||||| ||||| |  | | |||||||  ||| |  |||  ||   |  |  |  | |||   |||| |  |   | |  |        || |                         
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|67016408|gb|CO445157.1|CO445157
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
EST: gi|71417754|gb|DR804198.1|DR804198
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
EST: gi|6020391|gb|AW065319.1|AW065319
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGNGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAG
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAG

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), 47 (downstream exon)
Score: 82

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 44

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 82

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG