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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacgcttgccattttatggaagcattcatgttccactttcccgtttttaatgtgcttctgcttttctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA

Basic information

species Zea mays
transcript GRMZM2G135904_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135904_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 3
gtaagacgcttgccattttatggaagcattcatgttccact-ttcccgtttttaatgtgcttctgcttttctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA
|||||  ||||   ||   ||   | ||||| | ||  | | ||   ||| |||||     | || | | || | ||||||| ||||| ||||| ||||||||||| ||||||||| ||||||| || ||||||||||||
gtaaggtgcttat-atgagatttta-cattcctctttaagtctttatgttattaat-----tatgttctactttgtgaagGATTATGTTGCAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA
















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|67016391|gb|CO445140.1|CO445140
EST:     GACTTGCCCGTGCATCATTCAACGATGCCCCTTCAGCTATATTTTGGACA                         GATTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT
genomic: GACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT
EST: gi|22545672|gb|BU098031.1|BU098031
EST:     GACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACA                         GATTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT
genomic: GACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT
EST: gi|61118794|gb|DN559755.1|DN559755
EST:     GACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACA                         GATTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT
genomic: GACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTT

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), 48 (downstream exon)
Score: 119

CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

CAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAATGATGCCCCTTCAGCTATATTTTGGACAgtaagacgct ... ctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcattcatgttccactttcccgtttttaatgtgcttctgcttttctgtttgaagGACTATGTGGCAACAAGGTGGTACCGGGCACCTGAACTATGTGGTTCCTTTTTCTCCAAA
                        ttttaat  putative branch site (score: 99)
                                  cttctgcttttctgtt  putative PPT
                       tttttaatgt  TA-rich tract