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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattactatagtcatgataatcatttcgttatttatctgatgaaccatctaatttacttttgttcctatatactctttgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT

Basic information

species Zea mays
transcript GRMZM5G897368_T01
intron # 1
splice site 3'
intron type U2

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|31356670|gb|CD441027.1|CD441027
EST:     CTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAG                         GATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCAT
genomic: CTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAGgtacattact ... tgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCAT




















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: 42 (upstream exon), 39 (downstream exon)
Score: 10

ACATAAGAGTCAGGATGCTAATAATAGTAATGCTCCTGATGGTGTATTAGCTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAGgtacattact ... tgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

ACATAAGAGTCAGGATGCTAATAATAGTAATGCTCCTGATGGTGTATTAGCTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAGgtacattact ... tgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 33

ACATAAGAGTCAGGATGCTAATAATAGTAATGCTCCTGATGGTGTATTAGCTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAGgtacattact ... tgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 27

ACATAAGAGTCAGGATGCTAATAATAGTAATGCTCCTGATGGTGTATTAGCTGATCAGTGGGTTGCGCTTGTCAATAATTGGATGACCCCTAAAGCACAGgtacattact ... tgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgatgaaccatctaatttacttttgttcctatatactctttgtttcgtagGATTTAAGTGAGGCCAATAGGATAAATTGTACAAGAAGAAAGTCAATGCATACATCTGGAACAAAAAGCTTTGCTCGGAGTAGAGAAGAATTGGTATTAT
              atctaat  putative branch site (score: 27)
                                        ctctttgtttc  putative PPT
              atctaatttactttt  TA-rich tract