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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcccctccccgatcccgtccgccttcgccagttcaattgtgtcgttttttgttcggtgggtggcgtgggaggaggaatcacggagcagcgtct...

Basic information

species Zea mays
transcript GRMZM2G159295_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159295_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 1
CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcccctccccgatcccgtccgccttcgccagttcaattgtgtcgttttttgttcggtgggtggcgtgggaggaggaatcacggagcagcgtct------
|||||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||| | |  ||||    |   |||| ||| ||||  | |      | |   |||   | | || ||||   |||||   |  | ||  ||   | |||  |      
CGTCGACATCAACGCGCGCGACCTGCGCATCCTCGACCCGCTGCTCTCCTACCCATCCACCATCCTCGGCCGCGAGCGCGCCATCGTCCTCAATCTCGAGgttcgcgccccccaatcc-ccccgcccgacttcatccg---ggattttcggttcgatatgcgatggg-atcgtggagcgccggatt-cgtgacggcgaattcccgg
















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|32843052|gb|CD982733.1|CD982733
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|149107575|gb|EE189457.2|EE189457
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|110941263|gb|EE161420.1|EE161420
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCCACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|26557372|gb|CA829607.1|CA829607
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|32843159|gb|CD982840.1|CD982840
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|29544404|gb|CB604784.1|CB604784
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG
EST: gi|32836386|gb|CD976064.1|CD976064
EST:     ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAG                         CATATAAAGGCGATCATCACTTCCAACGAG
genomic: ACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 19

CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 45

CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG


Block sizes: 10 (upstream exon), 49 (downstream exon)
Score: 17

CGTCGACATCAACGCGCGCGACCTCCGCATCCTCGACCCGCTGCTATCCTACCCCTCCACAATCCTCGGGCGCGAGCGTGCCATCGTCCTCAATCTCGAGgtgcccctcc ... gctcgagcagCATATAAAGGCGATCATCACTTCCAACGAG