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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatagctactctttgaggttctgctcatgtctaataggtcgtagtctaaaccatacagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 10
gtacata-tagctactctttgaggttctgctcatgtctaataggtcgtagtctaaaccatacagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA
||| | | ||  ||  | ||||  || | |   |   ||||         |  |||   | | |||||||||||||| ||||||||||| || ||||||||||| || |||||| ||||||||||||||||| |||||||||||||||| || 
gtataaaatatatagccattgaaattatacaggttcgtaatgcacaacccta-aaattgtgccgtttgcagGTCTGCTGCTGTTGATTCAAGTGGTCGTGAGTTAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAG
















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|211441851|gb|FL182588.1|FL182588
EST:     CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAG                         GTCTGCGGCTGTTGATTCCA-GGGTCGTGAGTTGAATCGTAACCGATTGAT
genomic: CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
EST: gi|32933693|gb|CF038505.1|CF038505
EST:     CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAG                         GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
genomic: CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
EST: gi|60341753|gb|DN208726.1|DN208726
EST:     CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAG                         GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
genomic: CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
EST: gi|32832812|gb|CD972490.1|CD972490
EST:     CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAG                         GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
genomic: CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
EST: gi|33094155|gb|CF054149.1|CF054149
EST:     CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAG                         GTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT
genomic: CTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGAT

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: 219

TTCCCAACCCTGAGGACAAAACCGCAATGAAGTTTATTACACAAGCAGTTCTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 402

TTCCCAACCCTGAGGACAAAACCGCAATGAAGTTTATTACACAAGCAGTTCTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

TTCCCAACCCTGAGGACAAAACCGCAATGAAGTTTATTACACAAGCAGTTCTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

TTCCCAACCCTGAGGACAAAACCGCAATGAAGTTTATTACACAAGCAGTTCTTGATAACAAGGCAGACTTAGGCATCATATTTGATACTGATGTTGACAGgtacatatag ... cagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgaggttctgctcatgtctaataggtcgtagtctaaaccatacagtttgcagGTCTGCGGCTGTTGATTCCAGGGGTCGTGAGTTGAATCGTAACCGATTGATTGCTTTGATGGCTGCCATAGTTCTTGAGGAA
                                 gtctaaa  putative branch site (score: 385)
                   tctaata  TA-rich tract