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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG

Basic information

species Zea mays
transcript GRMZM2G127050_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 3'ss of exon 7
gtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG
|||||  |   ||||| ||   || |||     ||   | |  |   |   | | | | |      | |  |  | || | |||||||||||||||||||||||| |||||||||||||| ||| | || |||||||||||||| |||||||| || ||||| |||||||| ||| |||||||||
gtaaat-attggagcactttgatttctgtcatatggcagatcgttgtctaagaaatctatctcttcatcaatctccctgttgcagCTATCGTTCCAGGAATGGACTCAGCAGATGAGGGATATGTTAGATGCTAGGAAACGTGGAGACTTTGCGTTTCGTGATAAAGATTTTAAGACAGCCATAG

upper sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 5
gtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcg---cagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG
||||  ||   | |||||      | |      | ||   || |     || |  |||   | ||     |    |  || |   ||| | |||||||| || ||||| || |||||||| || |||||||| || ||||| ||||| |||| ||| ||||||||||| || || ||| ||||||| |
gtaactgatgggtgcattg----ggtttaaatttacta--tttttggttggatgatatgccataaggtttgaatttggattggttcagTTGTCGTTCCAAGAGTGGACTCAACAGATGAGAGATATGCTGGAGGCAAGGAAGCGTGGAGACTATGCATTCCGTGACAAGGACTTTAAGACAGCCATTG

upper sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG
|||   ||      ||  | |     ||| |    |   |||     |   |    ||     |||     ||    ||  |||| |||| ||||| |||||||| || || ||||| || ||||| || || || || ||||||||||| || ||||||||||||||||| ||  |||||||||
gtacttgatttctacagatgtaggtttgcagatccccatctttaattctatgctaaattctttaaatgta-tgtggataatgcagTTATCTTTCCAAGAATGGACACAACAAATGAGAGATATGCTTGAGGCAAGAAAGCGTGGGGACTTAGCATTCCGTGACAAAGATTTTAAAACAGCCATAG

upper sequence: GRMZM2G127050_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 7
--------gtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG
        ||    ||  |  |  ||| | | ||  ||   | ||      ||||  ||  | |   | |       | ||  |   |  ||| | || ||||| |||||||| || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| ||  | ||||| |
gtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtggtttatcttggtgttgtattggtt-cagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTG

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: 55

TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAG
                                           cctctatc  CT-rich tract
                             taagaaaaa  TA-rich tract