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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatattgtgtcagagctagtatacctatacacatgttccatctttcatttcagaaacttcatgctgatgacgaattatacttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA

Basic information

species Zea mays
transcript GRMZM2G132084_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132084_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
gtaagtatattgtgtcagagctagtatacctatacacatgttcc----atctttcatttcagaaacttcatgctgatgacgaattatacttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA
|| || ||    ||  |||||||||| |  |||       | ||    || |||| ||||  ||| |||||  | |  || | |||  | | ||| |||||||||||||| |||||||| || |||||||| ||| ||||||||||| |||||| ||| || ||||||||||| ||| |  | ||||||||||| |||
gtcagcat----tgctagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtta--cctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
















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|211442016|gb|FL419342.1|FL419342
EST:     AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAG                         GGGTATGTCCAGCGCACATGCAATTTTTAT
genomic: AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTAT
EST: gi|78076717|gb|DV505151.1|DV505151
EST:     AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAG                         GGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT
genomic: AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT
EST: gi|211506260|gb|FL375259.1|FL375259
EST:     AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAG                         GGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATA
genomic: AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATA
EST: gi|38687922|gb|CK144953.1|CK144953
EST:     AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAG                         GGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT
genomic: AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT
EST: gi|101387192|gb|EB815613.1|EB815613
EST:     AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAG                         GGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT
genomic: AAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATAT

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), 49 (downstream exon)
Score: 29

GCTTATGATTTCACTCGAATACTGAGCTCCTTTTATTTCAAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 12

GCTTATGATTTCACTCGAATACTGAGCTCCTTTTATTTCAAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA


Block sizes: 33 (upstream exon), 46 (downstream exon)
Score: 5

GCTTATGATTTCACTCGAATACTGAGCTCCTTTTATTTCAAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 24

GCTTATGATTTCACTCGAATACTGAGCTCCTTTTATTTCAAGGGGTATACTTTATTGACAAAAATACAGCGCATCGAATGGAACAATAGgtaagtatat ... cttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccatctttcatttcagaaacttcatgctgatgacgaattatacttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA
                           tgctgat  putative branch site (score: 24)
                                             cttgtttt  putative PPT
                                      aattatacttgtttta  TA-rich tract