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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttttatgcacatgatgttatctttattttgattgaagtcctatcaagtgctacctgttgaagaattggatgttgtcaactaatgcacattgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG

Basic information

species Zea mays
transcript AC199571.3_FGT004
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC199571.3_FGT004 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 4
atgttttatgcacatgatgttatctttattttgattgaagtcctatcaagtgctacctgttgaagaattgga--tgttgtcaactaatgcacattgt--ttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGC--CCCATG-
   ||| ||  |  || ||     ||   | |     ||     ||    |  || || |  |||         |||||| ||    |   | ||||  |||||  |||||||| |||||||||||  ||||||| || ||||||||||| ||  |||||||||| |||||  |||||||||||||     | |    || || 
---tttcat-tatttgttgaacagttggctattggcaaaccaacatgctatattagctttcaaagtcccaacactgttgtaaatctttctgccttgtctttcagCCACCAATGTAAAGATAGCTGCAGTTCCTTCTAGTGTCGTGGTTCTTACCCCAGAGACCTTCGACTCTGTTGTCCTTGATGAAACCAAAGATGTCCTTGT
















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|149078743|gb|EE167547.2|EE167547
EST:     CATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCG                         GTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTT
genomic: CATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCGgtaagaccga ... attgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTT




















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: 53

TACCGCAAGGGCCTGTGGTCGCTGGAGGAGGACCAGAAGCTCCGCGACTACATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCGgtaagaccga ... attgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

TACCGCAAGGGCCTGTGGTCGCTGGAGGAGGACCAGAAGCTCCGCGACTACATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCGgtaagaccga ... attgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

TACCGCAAGGGCCTGTGGTCGCTGGAGGAGGACCAGAAGCTCCGCGACTACATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCGgtaagaccga ... attgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

TACCGCAAGGGCCTGTGGTCGCTGGAGGAGGACCAGAAGCTCCGCGACTACATTCTCCTCCACGGCCACGGCTGCTGGAGCGCGCTCCCCATGAAAGCCGgtaagaccga ... attgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtgctacctgttgaagaattggatgttgtcaactaatgcacattgtttcagGTACCAATGTCAAGATAGCTGCCATTCCTTCAAGCGTCGTGGTTCTGACTTCAGAGACCTTTGACTCAATTGTCCTTGATGAGTTTTATGCCCCATG
                                  aactaat  putative branch site (score: 28)
                                              ttgtttc  putative PPT
                 aagaatt  TA-rich tract