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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

Basic information

species Zea mays
transcript GRMZM2G180328_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgt-ctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
 ||    || | | |      | | |  | |  |      |    |  || ||     | ||        | | |  | || |   | ||  || |||  | || ||| |||||  ||||||| ||||| |||||||| || ||| | ||| |||||||||||||||||||||| ||||||||||||||  |||| ||  |||| ||
-ta-aaatcttgcacaaattattctcataattctgaaataaatgataataactt-ttttttattgataaataatt--taatat--attctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
                          | |  | || |       |||| |  |   | | | | |  | || | | |     |   |   | || | | ||| ||||  ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| ||  |||||||||| || || ||  |||| ||
--------------------------gtaa-cattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttat-tgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatc-tcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
                     | |    | |  |  |    |||||| |     | |    ||    |||  | | |   |  | | || |      |    |||||  || |     ||||||||||| || ||||||||||| || || ||||| || || ||||||||||| || ||||||||||| ||||||||   ||| ||
--------------------gttcgtttaatt-tcttatggggtttcgttttgtgactgcaactaattgcatagttcaattgattgataatgagttggatgatgcagAAATTGGCTACTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGATCGGAAATACCCGAACGGTTCACGGCCGAACCGTGCCGCCGGAAGCGGCTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgc-cgctccacgcagt-cgttgttccaggtttcttagctc-------gccctgtacctgctgc------tgactcctgatctcgg-----tactactgctgtct----gtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
|||| | |  | |    | | ||| |  |  |   || ||     ||| |||  |        | | |    || || |      |  |||   | ||        || || |  ||| |    || ||| |||||| || ||||| ||||| ||||||||||| ||||| || || ||||| || ||||| ||||| ||| | |||||||| || |||||   ||||||
gtacctttttttcttttctcactctagtctctgtattcttttgccttttttaatttcattagggtcttaattctactacattttttttctctccaccttaaagtcctattatttatgtttttatgtacagAGATGGCTCTTTACGGTGAGAAAGAGTGGTACTTTTTCTCTCCTCGAGACCGAAAATACCCAAACGGTTCGAGACCGAACCGGGCTGCCGGAAGCGGGTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatc-tcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
         || ||     | | |     |   | |||    ||     | |     |      |   | | | | |   |  | | |  |      |||  |||||  || |   | ||||||||||| || ||||||||||| || || |||||||| || ||||||||||| || ||||||||||||||||||||   ||| ||
---------gttcgtt-tagtttcttatgggtttcgttttgtgt---gaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 1
------------------------------------------------gtacgtgtcgtccgccgccgctccacgc-agtcgttgttccaggtttcttagctcgccctgtac------ctgctgctgactcctgatctcggta-ctactgctgtc----tgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
                                                |    | |  | ||    |  ||   || |  | |     |    || | |    |   | ||        |  |  | |    | || |   |  ||  || ||||    | |||||| |||||  ||||||| ||||| |||||||| || ||| | ||| |||||||||||||||||||||| ||||||||||||||  |||| ||  |||||||
gtaacagtaatacacaaatcgaatccattatctttttttctctcctctgcgactttttttcgttttccttctctgctaaccatcagatccaccttataattctgaaatatataatatttttttattaataaataattttattttcttttggtgtcgtgttatgcagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGAACCGGGTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgt----ctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
                        ||  | || ||  | ||  ||  ||   ||   |  |  ||| | || | |  | || |    | |  | ||||    || | ||||  ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| ||| |||||||||| || || ||| |||| ||
---------------------gtaacataatcattcattca--ttcattcattc-ttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA

upper sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA
       |  |   |             | ||  |    |   | |||      ||    |  | |   |||| |   ||| |   |   | ||  || | |||||| ||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| ||  |||| ||||| || |||||  |||| ||
-----aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgg-gtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

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: 41 (upstream exon), 48 (downstream exon)
Score: 29

GTGGTGCACTACCTCTGCCGGCGCTGCGCCGGGCTGCCCATCTCCGTGCCCATCATCGCCGAGGTCGACCTATACAAGCACGATCCCTGGCAGCTCCCAAgtacgtgtcg ... gtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 281

GTGGTGCACTACCTCTGCCGGCGCTGCGCCGGGCTGCCCATCTCCGTGCCCATCATCGCCGAGGTCGACCTATACAAGCACGATCCCTGGCAGCTCCCAAgtacgtgtcg ... gtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 207

GTGGTGCACTACCTCTGCCGGCGCTGCGCCGGGCTGCCCATCTCCGTGCCCATCATCGCCGAGGTCGACCTATACAAGCACGATCCCTGGCAGCTCCCAAgtacgtgtcg ... gtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GTGGTGCACTACCTCTGCCGGCGCTGCGCCGGGCTGCCCATCTCCGTGCCCATCATCGCCGAGGTCGACCTATACAAGCACGATCCCTGGCAGCTCCCAAgtacgtgtcg ... gtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA