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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattgtgttgtctgcatgaaattttcaaaatgttttagtcccgtgttgttctgttaagtagcttgttacgccaatgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG

Basic information

species Zea mays
transcript GRMZM2G121427_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121427_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 11
-----------------gtatgcattgtgttgtctgcatgaaattttcaaaatg----ttttagtcccgtgttgtt--ctgttaagtagcttgttacgccaatgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG
                 ||| |  ||   |    ||||     | ||  |         || | || |   ||| |  ||||||| |   || |   ||  |||| |  || |||| ||||||||||| || ||||| ||||| |||||||||||||||||||| ||| ||||||| ||||||||||| |||||    |  |  ||||  |
gtaattacggcatctctgtaggagtttcctaacatgcactttgtctttgatgcacaatcttgattctcagcttgatgtctgttaattgtgttttcgtgctgatgagtttagGTCAGATTGAGCAAGAACTATCGCTCTACACGGGCAATTGTTGAAGCAGCAACAGCTTTAATTCACAACAACACTAAACGGCAAAGCCACAAACTTGCTG
















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|18384991|gb|BM418190.1|BM418190
EST:     ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAG                         ATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
genomic: ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
EST: gi|88758498|gb|DY542867.1|DY542867
EST:     ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAG                         ATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
genomic: ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
EST: gi|20802387|gb|BQ293437.1|BQ293437
EST:     ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAG                         ATCAGGTTGAGCAAGAATTACCGTCTCTACACGTGCAATTGTTGAAGCAGC
genomic: ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCG-CTCCACACGTGCAATTGTTGAAGCAGC
EST: gi|18053134|gb|BM318792.1|BM318792
EST:     ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAG                         ATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
genomic: ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA
EST: gi|78545014|gb|DV622512.1|DV622512
EST:     ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAG                         ATCAGGTTGAGCAAGAATTACCGCTCTACACGTGCAATTGTTGAAGCAGCA
genomic: ATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCA

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: 44 (upstream exon), 49 (downstream exon)
Score: 19

TCCATCTTCAGTTTCAATGGTGCCGATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG


Block sizes: 44 (upstream exon), 11 (downstream exon)
Score: 5

TCCATCTTCAGTTTCAATGGTGCCGATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 10

TCCATCTTCAGTTTCAATGGTGCCGATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 11

TCCATCTTCAGTTTCAATGGTGCCGATGTATCTGGCTTTGATTCATTTCGTAAAGATTTTCCGGATCATAAAGAGgtatgcattg ... atgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttttagtcccgtgttgttctgttaagtagcttgttacgccaatgactgcagATCAGGTTGAGCAAGAATTACCGCTCCACACGTGCAATTGTTGAAGCAGCAACTGCTCTAATTCAGAACAACACTAAGCGGCATCATCCTAGGCTTGTAG
                         ttaagta  TA-rich tract