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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgtatttctgcgagtgtattatgaaagcatactatgctaactcagttatttacttgctatgacttatgcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG

Basic information

species Zea mays
transcript GRMZM2G401934_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G401934_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g09000.1 (Oryza sativa), 3'ss of exon 3
gtatgctgta--tttctgcgagtgtattatgaaagcata-ctatgcta-------actcagttatttacttgctatgacttatgcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG
|| ||    |  | |||||  |  |   || || ||||| ||||||||       |  ||  |||||| ||  ||| |||| ||||||||||||||||| ||||||||||||| || ||||||||||| || || ||||||||||||| | ||||||||||| ||  ||||||
gtctgggaaaactatctgcatgccttgaattaacgcatagctatgctagactgccagccatatatttattttgtattacttgtgcttctgaaggcagCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAG
















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|211420915|gb|FL387494.1|FL387494
EST:     TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAG                         -C---TCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
genomic: TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
EST: gi|71430480|gb|DR811530.1|DR811530
EST:     TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTC-AA-                         --AGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
genomic: TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
EST: gi|211080316|gb|FL423993.1|FL423993
EST:     TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAG                         -C---TCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
genomic: TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
EST: gi|211201984|gb|FL401723.1|FL401723
EST:     TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAG                         -C---TCTAGTGGTGGATCCGG
genomic: TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGG
EST: gi|211204885|gb|FL411800.1|FL411800
EST:     TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAG                         -C---TCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT
genomic: TGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTT

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: 43 (upstream exon), 49 (downstream exon)
Score: 197

GTGAAAACAGGGATGCTCCCTTCAGCTGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 180

GTGAAAACAGGGATGCTCCCTTCAGCTGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTGAAAACAGGGATGCTCCCTTCAGCTGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 150

GTGAAAACAGGGATGCTCCCTTCAGCTGGAGTAGTCAAAGTTCTGTGTGAGAGTCTTAGGAAGTTTCCAGTCAAAGgtatgctgta ... gcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagcatactatgctaactcagttatttacttgctatgacttatgcttctgaagGCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAG
            tgctaac  putative branch site (score: 150)
                                            tgcttct  putative PPT
                       ttatttactt  TA-rich tract