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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttggttggatatatgctgtttaagcattgtattattggagtatatattttattcagtttctcgtatgcatcttttttcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG

Basic information

species Zea mays
transcript GRMZM2G102196_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102196_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g06270.2 (Oryza sativa), 3'ss of exon 9
gttgttggttggatatatg--ctgttt--aagcattgtatta---ttggagtatata---ttttattcagttt----------ctcgtatgcatctt-ttttcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG
||  |||||| |||||||   ||||||  || |||||| | |   |    ||| | |   ||| | || || |          ||  ||||  | || | |  || |||||||| |||| ||||| ||||||||||| ||  |||||||||||||||||||||||||  |  | || ||
gtatttggtttgatatataaactgtttgaaaccattgtttcacattccatgtaaacacactttaaatctgtctgctatccactctgatatgtgtgttatgtcttttggcagGAAATTCTGAGCCCATCAATTGAGCGAATCTGCACATACGTGGATAATTTGGCAGTTCTGCAGTCAAG
















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|61119836|gb|DN560797.1|DN560797
EST:     GCACAAGCAGTTCTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCATCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|60354570|gb|DN221543.1|DN221543
EST:     GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|4621437|gb|AI612270.1|AI612270
EST:     GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|60339229|gb|DN206202.1|DN206202
EST:     GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|31352028|gb|CD436385.1|CD436385
EST:     TTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCATTACTTGAGCGGATACACACATACGTGGATAATTTG
genomic: TTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|60340698|gb|DN207671.1|DN207671
EST:     GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: GCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
EST: gi|60337011|gb|DN203984.1|DN203984
EST:     CACAAGCATGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAG                         GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG
genomic: CACAAGCA-GTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTG

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: 103

TGACGAGCTGGAGAGATGCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

TGACGAGCTGGAGAGATGCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TGACGAGCTGGAGAGATGCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG


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

TGACGAGCTGGAGAGATGCACAAGCAGTTTTCTGAAGTTGACCAAGCATCATCTTTCCTATTTCAAGgttgttggtt ... tcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattggagtatatattttattcagtttctcgtatgcatcttttttcttgggcagGAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG
                                  tgcatcttttttctt  CT-rich tract
       agtatatattttattc  TA-rich tract