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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCCCCGATCTCGCCGTGCCCTACCCCCAGCCTCGCTCCGCCGCCACCAGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatccgcccacggcccactcgcccgcccaacccggttctccctccaccctccagcaacctcgcgcctcagcgacccgccgaccccatcgcttggcttcgctttgggactgggggttagttgattggtcggttgattgatcgatctagtgctcgatcctcgcag

Basic information

species Zea mays
transcript GRMZM2G007555_T01
intron # 1
splice site 5'
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|149111971|gb|EE191131.2|EE191131
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|60347262|gb|DN214235.1|DN214235
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|149077489|gb|EE166185.2|EE166185
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|71319028|gb|DR796259.1|DR796259
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|148944608|gb|EC889738.2|EC889738
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|211074512|gb|FK958797.1|FK958797
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|211321608|gb|FL062350.1|FL062350
EST:     GGAGAGATCGCGCCCCCCATTCCCACAATCTAATGCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|93014305|gb|EB639825.1|EB639825
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
EST: gi|101386442|gb|EB815238.1|EB815238
EST:     AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAG                         GAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA
genomic: AGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGA

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), 48 (downstream exon)
Score: 168

TGGCCCCCGATCTCGCCGTGCCCTACCCCCAGCCTCGCTCCGCCGCCACCAGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGAGTGGCGTGGGGCAGGGAGCCGGTGGCGAGGGCATATCATGGTGCAGTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

TGGCCCCCGATCTCGCCGTGCCCTACCCCCAGCCTCGCTCCGCCGCCACCAGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGAGTGGCGTGGGGCAGGGAGCCGGTGGCGAGGGCATATCATGGTGCAGTGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 75

TGGCCCCCGATCTCGCCGTGCCCTACCCCCAGCCTCGCTCCGCCGCCACCAGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGAGTGGCGTGGGGCAGGGAGCCGGTGGCGAGGGCATATCATGGTGCAGTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

TGGCCCCCGATCTCGCCGTGCCCTACCCCCAGCCTCGCTCCGCCGCCACCAGAGAGATAGCGCCCCCCATTCCCACAATCTAATCCTTCCGTCCCTCGAGgtaaacatcc ... atcctcgcagGAGCCGAGCCCTCCGCGCGGCCGTGGGATGGGGCGGTGACAACACCGGTGAGTGGCGTGGGGCAGGGAGCCGGTGGCGAGGGCATATCATGGTGCAGTGC