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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaactgttcccaactcccaagaaggatgtattcatatccttgactgatgaagtatgctgcgccaattgctaatcagttgccctacctcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC

Basic information

species Zea mays
transcript GRMZM2G034833_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034833_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 4
gtaaaaaactgttcccaactcccaagaaggatgtattcatatccttgactgatgaagtatgctgcgccaattgctaatcagttgccctacctcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
||||| |    ||||  |  |     ||| || ||||| ||  ||||  || || | | |  |  |  ||||| | | |  || | || | ||     ||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||| ||||||  ||||| ||| | || || ||  |  | || |
gtaaatactgtttcctgaaact--gcaagcatatattcctagtcttgcatggtgta-tgtattcagttaattgtttaccttttcctctgcttc-----tgtagACAACATATGAGAACTTCAGGTATCGGTATGATCAACGGGCCAACCCATACAACAGGGGAGTCATGGAGAACATTAAAGATATATTCTTCTCTGCAATTC

upper sequence: GRMZM2G034833_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 4
gtaaaaaactgttcccaac-tcccaagaaggatgtatt-catatccttgactgatgaagtatgctgcgccaattgctaatcagttgccctacctcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
||||  |    ||   ||  ||   | |  |  ||||    ||   || |   ||  |   | | |  |      ||    | |||   | | |     ||  |||| ||||||||||||||||| || || ||||||| ||| |||||||| || |||| |||| |  |    ||  ||  | |||| || |  ||||  || |
gtaatcattcctttttaaaatctttatatagtagtataatttaaagttaagctatctatcctacaggacttgcaactttatatttgtgtt-cattactgttacagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACAAGGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC

upper sequence: GRMZM2G034833_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 4
gtaaaaaactgttcccaactcccaagaaggatgtattcatatccttgactgatgaagtatgctgcgccaattgctaatcagttgccctacctcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
                       ||| |   |   ||   ||||        |      |     |   || |||    | |||| | |  |    |||| |||| |||||||| |||||||| || || |||||||  |||||||||||||| ||    ||| |  ||   ||  ||||| |||| || |  | ||  || |
---------------------gtaagcacagttctttttaatccgcatgctctagctgttcagatgtatatggcttcatatttgctcca--ttattcttgcagACTACATATGAAAACTTCAGATACCGATATGATCGGCGAGCCAACCCATATAATGAAGGAGTGTTGAATAATTTCAAAGAGATATTCTGCATCAGCATTC

upper sequence: GRMZM2G034833_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 4
gtaaaaaactgttcccaac-tcccaagaaggatgtattcatatccttgactgatgaagtatgctgcgccaattgctaatcagttgccctacc--tcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
||||  |    ||   ||  ||   | |  |  ||||    ||     | | |  |  ||| || |   | |||| | |   |     |  |  |     ||  |||| ||||||||||||||||| || || ||||||| ||| |||||||| || ||||  ||| |  |    ||  ||  | |||| || |  ||||  || |
gtaatcagtcctttttaaaatctttatatagtagtata---atttaaaattaagtatctatcctactggacttgcaactttatatttgtgtccattactgttacagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACACAGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC

upper sequence: GRMZM2G034833_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaaaactgttcccaactcccaagaaggatgtattcatatccttgactgatga--agtatgctgcgcc-aattgctaa--tcagttgccctacctcggcctt--gtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
       |  |  | || || || |     |||  |   || ||   | |   |   |  ||  || ||| ||  ||  |  |    | | |||   |   |||  | |||| || |||||||| ||||| || || ||||||| |||||||||||| |||||||  ||| |  ||   ||| ||||  |||| || |  ||||  ||  
-----gtaacgggctcatcttcctaatgctatgattctgtagccgaaattttaggtcaaaatattgtgcctaacagcagaattttccttctctattccattcttttgcagACTACCTATGAGAATTTCAGATACCGATATGATCGACGAGCCAACCCCTACAACAAAGGAGTGGTGCAGAACTTCAAGGAGATATTTTGCACCAGCATTT

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: 203

GACCCCTGCATCTGTTGCTTTAATCATCTACACATTCATTGCGGTTTGGTTTGTTGGTGGCCTCTCTGTGTTCCATTTGTATCTCATGAGCACAAATCAGgtaaaaaact ... ggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 16

GACCCCTGCATCTGTTGCTTTAATCATCTACACATTCATTGCGGTTTGGTTTGTTGGTGGCCTCTCTGTGTTCCATTTGTATCTCATGAGCACAAATCAGgtaaaaaact ... ggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 22

GACCCCTGCATCTGTTGCTTTAATCATCTACACATTCATTGCGGTTTGGTTTGTTGGTGGCCTCTCTGTGTTCCATTTGTATCTCATGAGCACAAATCAGgtaaaaaact ... ggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GACCCCTGCATCTGTTGCTTTAATCATCTACACATTCATTGCGGTTTGGTTTGTTGGTGGCCTCTCTGTGTTCCATTTGTATCTCATGAGCACAAATCAGgtaaaaaact ... ggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgaagtatgctgcgccaattgctaatcagttgccctacctcggccttgtagACAACATATGAGAACTTCAGGTATCGCTATGATCAACGAGCCAACCCATACAACAGGGGAATCATGGTAAACATCAAACAGATCTTATTTACCACGATCC
                       tgctaat  putative branch site (score: 79)