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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgccttctttttcctgcagtgtttgagagttgacttgatactatcagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG

Basic information

species Zea mays
transcript GRMZM2G124051_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 5
----gtcagtgccttc-tttttcctgcagtgtttgagagttgacttgatactatcagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
     ||| || |    |||||  |  ||| ||  |   ||  ||| |||| ||  | ||  |||  |||||| ||||      ||| |||| ||||| |||||||||||||||||||||||||||||||||||||| || ||||||| |||  | ||| ||| ||| ||| |||||
gtatctcaatggcagggtttttgttatagtcttcaa---ttttcttcataccattcgtat--aatattttctgaacttca----atgtaggttgagTTTAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCAGCTGCTCAAAGAAAAGTGGCTTTAACTCGATTGATTAAG

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G39210.1 (Glycine max), 3'ss of exon 4
gtcagtgccttctttttcctgcagtgtttgagagttgacttgatactat-cagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
|| ||    |  ||| |      |||| ||| ||||  ||| |     | ||  |  || || | ||||       ||  |||||||| || || ||||||||||||||||||||||| |||||  | |||||  || |||| || ||    ||  | ||| |  ||||||||
gttagaaattgttttat------gtgtatgacagttctcttaagttagtacaaaacatagtgatgtctgt------ttgcatgcagGTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCGACCACTCAGAAGAAAACTGCCTTGAATAGACTGGTTAAG

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 4
gtcagtgccttctttttcctgcagtgtttgagagttgacttgatactat---cagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
||  |    |  ||| |      |||| ||| ||||  ||| |   | |   || |||  | || | ||||       ||  |||||||| || || ||||||||||||||||||||||| |||||  | |||||  || |||| || ||    ||  | ||| | |||||||||
gttggaaattgttttat------gtgtatgacagttctcttaagtttgtacacaacatagagtgatgtctgt------ttgcatgcagGTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAG

upper sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtgccttctttttcctgcagtgtttgagagttgacttgatactatcagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
     || |||  |||||      |   |     |  | ||    | ||  ||   |||  | |  ||| ||  | |  || ||||| |||||||| ||||||||||||||||| ||||| || ||||| ||||   | || || ||    ||| | ||||| ||||| |||
--gtatgtcttagttttctcctgttaccta----tctaattaggcccatttgc---taaatcat--tgggct--gct-catccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG

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|31360005|gb|CD444362.1|CD444362
EST:     GCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAG                         GTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGA
genomic: GCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAGgtcagtgcct ... ttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGA




















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: 61

GTGTACAGCGGAAGTCCTCAAGCAATTGATGGTTGCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAGgtcagtgcct ... ttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 48

GTGTACAGCGGAAGTCCTCAAGCAATTGATGGTTGCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAGgtcagtgcct ... ttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GTGTACAGCGGAAGTCCTCAAGCAATTGATGGTTGCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAGgtcagtgcct ... ttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 61

GTGTACAGCGGAAGTCCTCAAGCAATTGATGGTTGCGCTACTTTCTTTCGTCGGGACAGATTTTCGCATGTCAAAAAATATGAGgtcagtgcct ... ttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttgacttgatactatcagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
                       atctaat  putative branch site (score: 61)
                                        ctttgtt  putative PPT
                                         tttgttatat  TA-rich tract