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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggcttcatcttagctatatcaggaacactttgttgttctagacaactgctagaataatgcacccgattcactctgctacctcttcatgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA

Basic information

species Zea mays
transcript GRMZM2G099598_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099598_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 3'ss of exon 8
gtggcttcatcttagctatatcaggaacactttgttgtt-ctagacaactgctagaataatgc-acccgattcactctgctacctcttcatgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA
   | |  | | |    |||||||||||  | || |||| | | | ||  | |||| | | |  | |  | || || | |  ||||||   | ||||||| ||||| ||||| || |||||||| |||||||| ||||| || |||||| | ||||||||||||| |||||| ||||| || |||||||| || ||||
---gttggaacgtcaa-atatcaggaaccttctggtgttacaaaaaaatcgttagattgaagttatctcactc-ctttacctcctctttgggttgcagTTTGTTGATGTGGGAACAATGGTATCACCAACGGTATACGCTAGACGGAGCTTATGCCACCTCATGTCTGACCAACCTGATGCTGCCCTCCGGGATGCAA
















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|60397498|gb|DN230314.1|DN230314
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|8383297|gb|BE056240.1|BE056240
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|211493754|gb|FL287302.1|FL287302
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|50335562|gb|CO530688.1|CO530688
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|71762708|gb|DR960645.1|DR960645
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|74234524|gb|DT642438.1|DT642438
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|76016248|gb|DT943418.1|DT943418
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
EST: gi|149112519|gb|EE295384.2|EE295384
EST:     TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAG                         TTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC
genomic: TCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGC

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), 49 (downstream exon)
Score: 43

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 61

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 31

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAGATTGCTACACGCAGgtggcttcat ... catgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacaactgctagaataatgcacccgattcactctgctacctcttcatgctgcagTTCGTTGACGTGGGGACGATGGTATCGCCAACGGTGTACGCGAGGCGGAGCCTGTGCCACCTCATGTGTGACCAGCCTGACGCCGCCCTCCGCGACGCAA
                               ctctgctacctcttc  CT-rich tract
          tagaataat  TA-rich tract