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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattggtatctactcgtttttttcttctttttttttgtttaactaaaacggttgaatctatgttgttgtggacttgtggtccttgtgaatggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG

Basic information

species Zea mays
transcript GRMZM2G322953_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 3'ss of exon 8
ctattggtatctactcgtttttttcttctttttttttgtttaactaaaacggttga-atctatgttgttgtggacttgtggtccttgtgaatggtttgc--agTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG
    |   |  || | |  |||   | || ||| ||    | | ||      |  | || | | | ||| ||   |||   | ||| || |||||   |  |||||||||||||||||||| || || || ||||| || ||||||||||||||||| || || |||||||| |||||||| ||||| ||
---cttacagttatttgaatttgaatgctctttcttacactgaatactgaactgaacatttttttggttatgttgttgctctgcttctggatggtccacacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCG

upper sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 8
ctattggtatctactcgtttttttcttctttttttttgtttaactaaaacggttga-atctatgttgttgtggacttgtggtccttgtgaatggtttgc--agTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG-------------
    |   |  || | |  |||   | || ||| ||    | | ||      |  | || | | | ||| ||   |||   | ||| || |||||   |  |||||||||||||||||||| || || || ||||| || ||||||||||||||||| || || |||||||| |||||||| ||||| ||             
---cttacagttatttgaatttgaatgctctttcttacactgaatactgaactgaacatttttttggttatgttgttgctctgcttctggatggtccacacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCGGTATGCTGATGCA

upper sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
-ctattggtatctactcgtttttttcttctttttttttgtttaactaaaacggttgaatctatgttgttgtggacttgtggtcct-tgtgaatggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG
 || || || |   |  | | | |   | ||   | |  | |   |       |  ||      || || |  | || |  |  |    ||||| ||| ||| ||||| ||||||||||| ||||| ||||| ||||| || || ||||||||||| || ||  ||||||| || ||||| ||||| ||
gctctttgt-tgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttcta-atttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

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|32861683|gb|CF001365.1|CF001365
EST:     AAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAG                         TATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTA
genomic: AAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTA
EST: gi|74034973|gb|DT535463.1|DT535463
EST:     AAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAG                         TATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTA
genomic: AAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTA

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), 38 (downstream exon)
Score: 4

ATTCGTGGAGAAATGCAAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 64

ATTCGTGGAGAAATGCAAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 41

ATTCGTGGAGAAATGCAAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

ATTCGTGGAGAAATGCAAGTATCCTGAGGATGGTTCACCGCCTAGATCCTTGAGATATATCGGAAGgtgatccatt ... tggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacggttgaatctatgttgttgtggacttgtggtccttgtgaatggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG
 aactaaa  putative branch site (score: 46)
          aatctat  TA-rich tract