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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTACGCCTGGGGGTGAGGGTCAGGGTGGCGCCGGCGTGCAGGTGCAGGACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtgccattcgctcggccgatctctccgtagcttcccccatttctggcgcggtgtttatgtccgcattttaccgttctaccgaattgcacgtag...

Basic information

species Zea mays
transcript GRMZM2G032447_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|211282619|gb|FL407046.1|FL407046
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211230112|gb|FL407869.1|FL407869
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211500775|gb|FL109952.1|FL109952
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|149105705|gb|EE291269.2|EE291269
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211357709|gb|FL375125.1|FL375125
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211223919|gb|FL407824.1|FL407824
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACCAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|71428252|gb|DR809302.1|DR809302
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211048061|gb|FL385041.1|FL385041
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211273935|gb|FL428373.1|FL428373
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211217736|gb|FL411409.1|FL411409
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211500776|gb|FL109953.1|FL109953
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211480085|gb|FL429875.1|FL429875
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|211464166|gb|FL410745.1|FL410745
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
EST: gi|38687664|gb|CK144695.1|CK144695
EST:     ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAG                         GTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT
genomic: ACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTT

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), 46 (downstream exon)
Score: 41

CGCTACGCCTGGGGGTGAGGGTCAGGGTGGCGCCGGCGTGCAGGTGCAGGACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTTTCCAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 16

CGCTACGCCTGGGGGTGAGGGTCAGGGTGGCGCCGGCGTGCAGGTGCAGGACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTTTCCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

CGCTACGCCTGGGGGTGAGGGTCAGGGTGGCGCCGGCGTGCAGGTGCAGGACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTTTCCAAG


Block sizes: 40 (upstream exon), 46 (downstream exon)
Score: 26

CGCTACGCCTGGGGGTGAGGGTCAGGGTGGCGCCGGCGTGCAGGTGCAGGACGACCTCGCGCTGCCCCTCGGGATGTCGTTCGCGGCCGTCCTCGCGCAGgttcgtggtg ... tcatatacagGTTGTGAATACAAAGAATCGTTCAGGCGAAAGATTACAGCCTGCACTTCTTTCCAAG