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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggttctgcatgatattttagtggcaattctgattttttccatgatggctgtatgtttgaccttttgattcttgttatttgctgtctaatatatctgttcctacacaataatctcagtgtttatatgtagagtgtaacaaaaactgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG

Basic information

species Zea mays
transcript GRMZM2G019991_T01
intron # 7
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|211314558|gb|FL124188.1|FL124188
EST:     AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAG                         TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT
genomic: AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT
EST: gi|60338254|gb|DN205227.1|DN205227
EST:     AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAG                         TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT
genomic: AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT
EST: gi|211314557|gb|FL124187.1|FL124187
EST:     AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAG                         TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT
genomic: AAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTT

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: 45 (upstream exon), 47 (downstream exon)
Score: 52

GGAAAATCAGATGTTGGTAAAAAAAATATATGAACTTGATTCAAGACTACAAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 31

GGAAAATCAGATGTTGGTAAAAAAAATATATGAACTTGATTCAAGACTACAAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 46

GGAAAATCAGATGTTGGTAAAAAAAATATATGAACTTGATTCAAGACTACAAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 66

GGAAAATCAGATGTTGGTAAAAAAAATATATGAACTTGATTCAAGACTACAAGCACTTGAAGCAAAGGCTGCTCCTAGTGAAGCCTTAATGATTGAAAAGgtaaaggttc ... tgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacacaataatctcagtgtttatatgtagagtgtaacaaaaactgtaatgcagTTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG
                                gtgtaac  putative branch site (score: 66)
 tttatatgta  TA-rich tract