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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctcccactatttgctctctgtactttcattcaatcaacccctttggcactgtggttgtaatgctgttcaatctggaatggctag

Basic information

species Zea mays
transcript GRMZM2G162445_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162445_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 5'ss of exon 4
TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctcccactatttgctctctgtactttcattcaatcaa-cccctttggcactgtggttgtaatgctgttcaatctggaatggctag
|||||||| ||||||||  ||||| |    |||||| |||||||| || |||||||| ||||| |||||| | |||||||| || ||||||||||||||||||   ||     ||   |  | ||    |  ||||||| || ||  ||||    | || ||||||||||| | ||| ||||||   |||
TGTTCACTATTGCCCTGCTACTGGAGGTACTCTCTCACGTGAATACAGGGACATCACATCTTTCGTAGGCCTACCTACTGGTTCGGTTTATCCAACAAGGgtacattcttttgatcatccttttgctactctattcaatgaaacctatttgttgttttgtttgtaatgctgct-aatttggaatacttag
















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|211495775|gb|FL137513.1|FL137513
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTG
EST: gi|211495774|gb|FL137512.1|FL137512
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
EST: gi|211498656|gb|FL137521.1|FL137521
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
EST: gi|148956698|gb|EC902568.2|EC902568
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
EST: gi|211498653|gb|FL137518.1|FL137518
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
EST: gi|211498654|gb|FL137519.1|FL137519
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAN
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
EST: gi|211495776|gb|FL137514.1|FL137514
EST:     ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGG                         GATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG
genomic: ACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAG

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: 202

TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 44

TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 13

TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 49 (upstream exon), 21 (downstream exon)
Score: 10

TGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGGCTTGCCTACTGGCTCTGTTTATCCAACAAGGgtatgctccc ... gaatggctagGATGACAACGGCAACTTGTTGGTCACCGAGTATGGAATGTGTGAATATAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG