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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttctttctatctttaaaatttgccatgtcccaatataactaacttctgtttctcggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG

Basic information

species Zea mays
transcript GRMZM5G823484_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 19
gtagttttctttctatctttaaaatttgccatgtcccaatataactaact-tctgtttctcggttgtt-cagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG
||  | || | | |        ||| || |   | | | ||   |||||| | || || || ||| || |||||||||||||||||| ||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||
gtgttcttttatttgctcacctaatatgtccaatacaactaagcctaactatatgattatctgttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTG
















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|60356127|gb|DN223100.1|DN223100
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|9566477|gb|BE475986.1|BE475986
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|91878412|gb|EB408369.1|EB408369
EST:     GCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: GCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|32802642|gb|CD954878.1|CD954878
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTAGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|32804847|gb|CD957083.1|CD957083
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|71434510|gb|DR815560.1|DR815560
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|60396240|gb|DN229109.1|DN229109
EST:     CCAGATGATGGAGCTGCACCAGATCATCAGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
EST: gi|5847426|gb|AW000505.1|AW000505
EST:     CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG                         AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA
genomic: CCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGA

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: 145

GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 137

GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 101

GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAGgtagttttct ... ggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttaaaatttgccatgtcccaatataactaacttctgtttctcggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG
                           aactaac  putative branch site (score: 91)
                                       tttctcg  putative PPT
                      aatataactaactt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttctttctatctttaaaatttgccatgtcccaatataactaacttctgtttctcggttgttcagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG