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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcatgagcattactttaccccatgtgttccttagaaatactgtgttagcttccatcaatcttgatagatgctttctcggttgagataatatctgagaggattatctttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA

Basic information

species Zea mays
transcript GRMZM2G014788_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014788_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g19470.1 (Oryza sativa), 3'ss of exon 15
gtaggcatgagcattactttaccccatgtgttcc----------------ttagaaatactgtgttagcttccatcaatcttgatagatgctttctcggttgagataatatctgagaggattatctttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA
|||  || ||    ||||||  || |||| | |                 ||||||| | | | | | ||  ||||   | |||| || |  || | | |||| ||| ||||||||   ||| |||||||   ||||||||||||||  |||||||||| |||   |||||| ||||||||| ||| || |||||| | |||||||||||||| ||||| ||| | || |||||||
gtaaccaagaatgctacttttacctatgtatgctctgttttttatttgttttagaaagattatat-aactagcatcgtgcatgattgagg--ttatagattgatatagtatctgagt--attctctttgtgaacagTCACAAGTCAACCTTCATGGTAAGGTCCTGTGCAAAGAGCAATGCAACCAAAATATTCTGCTGTCACTTGTTAGATTAGCTGGGGGAATCGAGCAGGAAA
















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|31361460|gb|CD445817.1|CD445817
EST:     CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAG                         TCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAAGAGCAATGCAGCCAG
genomic: CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAG
EST: gi|31359820|gb|CD444177.1|CD444177
EST:     CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAG                         TCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAAGAGCAATGCAGCCAG
genomic: CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAG
EST: gi|78112628|gb|DV531022.1|DV531022
EST:     CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAG                         TCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAG
genomic: CTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAG

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: 231

ATTACCTGTAGATTCCGAACGCTCTTCTAGTCTTATGTTTTCACCGGGATCTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 207

ATTACCTGTAGATTCCGAACGCTCTTCTAGTCTTATGTTTTCACCGGGATCTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

ATTACCTGTAGATTCCGAACGCTCTTCTAGTCTTATGTTTTCACCGGGATCTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 182

ATTACCTGTAGATTCCGAACGCTCTTCTAGTCTTATGTTTTCACCGGGATCTATTAGCGTCAATGTAAATAGCCCGTTGCTTGATCTGGAATTCTCTCAGgtaggcatga ... ttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagatgctttctcggttgagataatatctgagaggattatctttgttggcagTCACAAGTCAATGTTCATGGTAAAGTCTCATGCAAACAGCAATGCAGCCAGAACATTCTGGTCTCACTTGTTAGATTGGCTGGCGGAGTTGAACAGGAAA
 tcttgat  putative branch site (score: 182)
                                       ttatcttt  putative PPT
                     agataatat  TA-rich tract