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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgacgtactactggcctgcgtcctcctcattattatccctattaatcagtacgcatttatacatacataacgtaaattctatggactaaaaaagagttacaagtaacttttaatctgaaacggagctaggaagtttgtaatgtcgtcgtcctctggcaataacttggccgtcgctaacgtacgtacgcgtgcag

Basic information

species Zea mays
transcript GRMZM2G070252_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070252_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g43010.1 (Oryza sativa), 5'ss of exon 3
-CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgacgtactactggcctgc--gtcctcctcattattatccctattaatcagtacgcatttatacatacataacgtaaattctatggactaaaaaagagttacaagtaacttttaatctgaaacggagctaggaagtttgtaatgtcgtcgtcctctggcaataacttggccgtcgctaacgtacgtacgcgtgcag
    | | |  |||||||||||| ||||||| ||| |||| | |||||| || ||||||||||||||||| ||||||||||| |||   || |||| |  ||||       |||| |   | |  |  ||  ||    || || | |||    ||    | | | |||         |   | | || |||  ||  |  |||   |||  ||                                                                                          
TTCGGAGTCC-CTTTATGTCAAGTTCATAGAAGAGTTGGATAAATGCATTCTTGGATATTTTGCGTTCCATTGGGACCATGCTACCGCTCTTATCAGCCAGgtatt-tattgtaccatgcgacaactggttttctgatttttttttcctggccatttacatggaatta---------agtttcacttttatatac--agtaagtactactggt------------------------------------------------------------------------------------------
















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|71441306|gb|DR822356.1|DR822356
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|149099789|gb|EE185842.2|EE185842
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|149101143|gb|EE187251.2|EE187251
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|148928766|gb|EC873522.2|EC873522
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|148961396|gb|EE012134.2|EE012134
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|8367234|gb|BE050179.1|BE050179
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|149089894|gb|EE179180.2|EE179180
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|67020546|gb|CO449295.1|CO449295
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGAAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
EST: gi|149077280|gb|EE165954.2|EE165954
EST:     TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCG                         GCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG
genomic: TCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 75

CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTGGAAGCAACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 87

CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTGGAAGCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTGGAAGCAACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 87

CGAGTGCCTGCTTTATGTCAAGCTCATAGAGGAGCTGGACAGATGCATCCTCGGATATTTTGCGTTCCACTGGGACCATGCCACCTACCTCATCACCTCGgtacgacgac ... acgcgtgcagGCCTTGACCGCGGACACCGGCAGCAAAAGGAAGCTCAGGAACATGGTCTTGGAAGCAACAAG