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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttatttttaactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 16
gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttatttttaactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT
   |    ||||   | | |  ||     ||| | ||||  | || |      | || ||||   ||| | |  |||||||||||||||||| |||||||||||||| ||||||||||||||||| || || |||||||| ||| | |||||||||||||||||| |
--gtaagtctctatctctatgtgtgcatgcacac-gtctggtgctcaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCGCACCT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 16
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttatttttaactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT
   |  | ||||   | | |  ||     ||| | ||||  | || |      | || ||||   ||| | |  |||||||||||||||||| |||||||||||||| ||||||||||||||||| || || |||||||| ||| | |||||||||||||| ||| |
--gtaaatctctatctctatgtgtgcatgcacac-gtctggtgctgaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
---------------gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttattttt----aactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT
                ||||        |||||| |   |  ||      ||||  | || ||  |||  | |||||    |  |||   |  ||||||||||||||||||||| || |||||||| |||||||||||||||||||| || |||||||| || || |||||  ||||||| |||||
gtatgctttatataactatgttatgtccatttttaataacgagaataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT

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|32929959|gb|CF034771.1|CF034771
EST:     CTCGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAAC
genomic: CTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGC
EST: gi|211502860|gb|FK981747.1|FK981747
EST:     CTCGTTAGTGATAACTGGATCGAGCCACCTAGAAKAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAAC
genomic: CTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGC
EST: gi|33094019|gb|CF054013.1|CF054013
EST:     CTCGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAG                         CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAAC
genomic: CTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGC

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: 333

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 159

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATCGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgcacct ... tcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatgacacgctgtctaatacttatttgaccttatttttaactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT
                                    ttttaac  putative branch site (score: 159)
              tctaatacttattt  TA-rich tract