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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcccgggctgcgcactctcttccccgagtttctgtctttcttccgccgcggacgtgcctctgacctgtgtgttttttgcag

Basic information

species Zea mays
transcript GRMZM5G825512_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825512_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g43540.1 (Oryza sativa), 5'ss of exon 1
CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcccgggctgcgcactc-tcttccccgagtttctgtctttcttccgccgcgga-cgtgcctctg----acctgtgtgttttttgcag
| |   |||||| ||||| || |||||||||||| |||||||||||| |||||||||||||||||||||||||| |||||| || || |||||||||||||| |||  || |||||     ||| | | |      ||| ||  |  |||    || ||  |||| |||||    | || |  | ||   ||||
CTCCCGCCTCGGCCTCTCCGGCTCCCGCCCCGTCGTCCGCAAGGCCGCCGAGCTCCGCCGCCTCTGCGACGTCACCTTCGACTCCTCCGTCCTCGGCATCgtgagcaaccggggctttttcctcctatgctgtttctttttggttggcttggctcgtggttcgtgtctctgagagatcttttggcttcgcgcag

upper sequence: GRMZM5G825512_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0026g02290.t01 (Vitis vinifera), 5'ss of exon 1
CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctg-cccgggctgcgcactctcttccccgagtttctgtctttcttccgccgcggacgtgcctctgacctgtgtgttttttgcag----------------------------------------------
   ||| || ||||| || |  |||   | | ||||||| || |||| |||||||||||||||||||||| || | ||||||||||||||| ||||  | || || |  |||   || |   |  || | | |     |  |  || |   |     | ||         |    |     |     |                                               
GAAGAAGCTAGGTCTATCCGATTCCAAACACATCATCCGAAAAGCCGCCGAGCTCCGCCGCCTCTGCGACATCCAGTTCGATTCTTCTGTCATCGGAGTTgtcagttttcccaatcttcattcattcattcaca----taagatttacacacaaaaagaacaaaaaaaaaaaaaataaaaataaaataaaaccaccaacgttgagtgctaatggagaaattttctcattttctag
















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|22472637|gb|BU037117.1|BU037117
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|211176728|gb|FL201368.1|FL201368
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|149098295|gb|EE184263.2|EE184263
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|211176726|gb|FL201366.1|FL201366
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|22542104|gb|BU092542.1|BU092542
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|87155630|gb|DY400419.1|DY400419
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|26457204|gb|CA828787.1|CA828787
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGC-AAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|71444691|gb|DR825741.1|DR825741
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
EST: gi|148954922|gb|EC900410.2|EC900410
EST:     AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATC                         GGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA
genomic: AGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 30

CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 8

CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 12

CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 3

CGCGAACCTCGGTCTCTCGGGGTCCCGCCCCGTCATCCGCAAGGCCGGCGAGCTCCGCCGCCTCTGCGACGTCAACTTCGATTCTTCTGTCCTCGGCATCgtaagctgcc ... ttttttgcagGGCGAGGTCTGCAAGGCCATCATCTGCCTGGAGATCGCCGCGTCCAA