Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatcccgtcccttttagaaatcaaatgataactgttctggattttttttaaaaaaaaatatatagttttgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA

Basic information

species Zea mays
transcript GRMZM2G033117_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 2
gtatgttatcccgtcccttttagaaatcaaatgataactgttctggattttttttaaaaaaaaat-ata----tagttttgatg-ccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA
|||||| ||||        |||       ||| || ||| |     ||| ||   | || ||| | ||     || ||  ||||  || | |  |||    |  || ||| | |  || ||||||| ||||||||| ||||||||||||||||||||||||||||||||||| | ||||||  | ||||||||||||||||||||||| ||||| ||||||||||||||||||||
gtatgtgatccaacttaccttatcttctgaatcatcact-tggcatattgttccgagaataaattcatgctgctatttacgatgatcaatatcaaataaccttctgatatataatcatatattgctgttctgcagGGTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGA
















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|148949364|gb|EC894819.2|EC894819
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|28361820|gb|CB240176.1|CB240176
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|149071591|gb|EE159982.2|EE159982
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|149102652|gb|EE288009.2|EE288009
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|78077999|gb|DV506414.1|DV506414
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|148932942|gb|EE285770.2|EE285770
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
EST: gi|149079919|gb|EE168929.2|EE168929
EST:     TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTG                         GTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC
genomic: TGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGC

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), 48 (downstream exon)
Score: 338

CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 272

CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 207

CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 151

CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatc ... tcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcagGTTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGA
 ttttgat  putative branch site (score: 151)
                                     tctattgctcttct  putative PPT
           tgtaatt  TA-rich tract