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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttcctctttcctatgcttttcgtagatccagctttcggcactgggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT

Basic information

species Zea mays
transcript GRMZM2G412899_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g17500.3 (Oryza sativa), 3'ss of exon 13
-----gttttcctctttcctatgcttttcgtagatccagctttcggcactgggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT
       |||  |    |  |   ||| | |           | |    |         ||  |||  ||   ||||||| | ||  || ||||       |||| | || || || ||||| |||||| |||||||||| |||||||||||||||||||||||  |||| |||||||| ||||| ||||  |||||||||||  
acaataatttggtagggcgcactatttacttgccatggttcattgtagttctaccatgattcgtatcgacgtcttgacatgctatgcttaaatgct-----gcagGTGGTAAATTTTTTTGTCAGTTTGTTGTTCTTGCGGCTTCTGGAGCAACTTGGTCCACAAGTTCTGTACACAATGTTTTCCTCAGCTTGTGTGGTAGCAG

upper sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G09270.1 (Glycine max), 3'ss of exon 12
--gttttcctctttcctatgcttttcgtagatccagctttcggcactgggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT
   ||| |    | |  |   | |||  | |   |  |    | |  ||    ||| |  |||  | || ||  |   || |   | ||||    |   ||| |  | || ||||||||| |  |  ||||||||||| | |||||| |||||||||||||||| || ||| | || ||| |  |  | ||  |  | ||  
ttctttgcaaactactaaaattgttctcataatgacttagaaggatgggaaagctcgtaatatggaatcctt--ctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG

upper sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 13
gttttcctctttcctatgcttttcgtagatccagctttcggcactgggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT
 || ||   | ||     || |||  | |   |  |    | |  ||    ||| |  | ||          |   ||||   | ||||    |   ||| |  | || ||||||||| |  |  ||||||||||| | |||||| |||||||||||||||| || ||| | || ||| |     | ||  |  | ||  
attatcacttatcagtatctgttctcataatgacttagaaggatcggaaagctcataatttattgaatcctgctctcaatagataaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCCATGTTTGCTATCTTTTGCATCATGGCAG

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|110961485|gb|EE181537.1|EE181537
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|78119069|gb|DV537453.1|DV537453
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|71760454|gb|DR958391.1|DR958391
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|71321128|gb|DR797263.1|DR797263
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|78110186|gb|DV528601.1|DV528601
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|71759302|gb|DR957239.1|DR957239
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|148974491|gb|EE025274.2|EE025274
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|101396769|gb|EB820310.1|EB820310
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|211453092|gb|FL443675.1|FL443675
EST:     CGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|76015719|gb|DT942889.1|DT942889
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|211329247|gb|FL462804.1|FL462804
EST:     GCTCTCTGCATGTCTGTACATTGG                         AYCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: GCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|50326105|gb|CO521231.1|CO521231
EST:     CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGG                         ATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
genomic: CTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTT
EST: gi|74240465|gb|DT648379.1|DT648379
EST:     ATGTCTGTACATTGG                         ATCGGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACT
genomic: ATGTCTGTACATTGGgtaagaactc ... aacttggcagATC-GTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 6

TTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGCATGTCTGTACATTGGgtaagaactc ... aacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT
                                         atgtaac  putative branch site (score: 6)
       tctttttata  TA-rich tract