Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaggctgagatttgttggacctatttcttttggatgccccaactagctttacaaaatgggtgattattttaaagagatctaatgcatcttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA

Basic information

species Zea mays
transcript GRMZM5G869993_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G869993_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g42050.1 (Oryza sativa), 3'ss of exon 27
tgaaggctgagatttgt-tggacctatttcttttgga--tgccccaactagctttacaaaatgggtgattattttaaagagatctaatgcatcttttattt--agACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA
  | |  |  |  |  | || |||||  | || || |  |    | || |   | |||  ||  || || ||| |  | ||| |||||| |  | ||  ||  || |||| |||||||||||||||||||| || |||||||| ||||||||||| |||||   || ||| |||||||| |||||  | || | |||||||||||
--atgctttggtctcatatgtacctaagttttgtgaacttatgtctaccaa--taacagcattagtaatcattattga-agaactaatgtacgtcttgcttgcagCCTGTAGACCAGCAACAACGCCTTTCGCAATGCTTCGACAAGCTGATGACTGATGTTGCTACGAATTTGGAACCAAAGAACAGAGATAAATTCACTCAAA
















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|33093809|gb|CF053803.1|CF053803
EST:     ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAG                         ACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACG
genomic: ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACG
EST: gi|33092039|gb|CF052033.1|CF052033
EST:     ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAG                         ACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACG
genomic: ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACG
EST: gi|32836639|gb|CD976317.1|CD976317
EST:     ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAG                         ACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGA
genomic: ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGA

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: 39 (upstream exon), 48 (downstream exon)
Score: 219

ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 161

ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 288

ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 131

ATGTTCAGTGAACTCAGAGCGCACATATTAGCATCACAGgttagagcag ... ttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctttacaaaatgggtgattattttaaagagatctaatgcatcttttatttagACTGTGGACCAGCAACAACGCCTTTCACAGTGCTTCGATAAGCTGATGACGGATGTCAATAGGAACTTGGAACCTAAGAATCGTGACAGATTCACTCAAA
                                 atctaat  putative branch site (score: 131)
                                           tcttttattt  putative PPT
                   attattttaaagagat  TA-rich tract