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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttatttttcttgtcctttctattccaaactatagttttgggatgttttaagttgattcattatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA

Basic information

species Zea mays
transcript GRMZM2G031352_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g68750.1 (Oryza sativa), 3'ss of exon 7
----------gtagttatttttcttgtcctttctattccaaactatagttt-tgggatgttttaagttgattcatt--atgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
           |   | ||||  |  |   |  || |||  || ||  ||| || | |   ||| |||||||||||  |  ||||||||||||||||||| ||||| |||||||||||||||||||| ||| |||| ||||| ||||||||||||||  ||| ||||||||||||||||||||  |
gtgattttaatttcctgttttcttcttatatcatactccgtaccatgttttctgtggtagattatgttgattcattctactttcagATAATATGCTGGGTTTTGGGAGAATATGGAACAGCAGATGGGAAATATTCAGCTTCATATATTATTGGGAAGCTGTATGATGTGGCAGAGGCCCACCCAA

upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 6
-----------------gtagttatttttcttgtcctttctattccaaactat---agtttt--ggga----------tgttttaagttgattcattatgtt-----cagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                  |  || |||||  |||  | | | | || |  | |   | ||||   |||          | |||||   | ||   |  |  |     ||| |||| || |||||  ||||||||||||| ||||| ||||||||  |||| ||||| ||||| | ||||||  | |||||||| ||||||||  |    |
gtagtttctaactttctatcctttttttttatgttttatatttccccacttgttttacttttcaaggagtcagatctgtcttttagcataatatgtagtactaattacagGTAATCTGTTGGGTTCTGGGGGAATATGGCACAGCTGATGGAAAGTATTCTGCTTCCTATATCACTGGGAAGCTATGTGATGTTGCAGAGGCATATTCAA

upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G35240.1 (Glycine max), 3'ss of exon 6
------------------gtagtt---atttttcttgtcctttctattccaaacta--------tagttttgggatgttttaagttgattcattatg---ttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                   |  ||   ||||| | |   | || || ||| ||  |        |  || | | ||   || |  |   | | |||    | ||| | || || |||||  |||||||||||||||||| |||||||||  |||| ||||| ||||| | |||||| || |||||  | ||||||||  |   ||
gtactttctatcccacttatgctttggattttcccttctcattttactccgaagaaattgaaagtgtttgtagaataactttaactctctaagtattgattgcagGTCATCTGTTGGGTTCTGGGGGAATATGGAACAGTAGATGGAAAGTATTCTGCTTCCTATATCAGTGGGAAGTTATGTGACATTGCAGAGGCATATTCCA

upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G35650.1 (Glycine max), 3'ss of exon 6
------------------gtagtt---atttttcttgtcctttctattcc----aaactata---gttt--tgggatg---------ttttaagt--tgattcattatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                   |  ||   ||||| | |   | || || ||     ||| || |   ||||  | | ||           |||||||  |||||    || | ||| | || || |||||  |||||||||| |||||||||||||||||  |||| ||||||||||| | |||||| || |||||  | ||||||||  |   ||
gtactttatatcccacttatgctttggattttaccttctcgttttactctgaagaaattaaatgtgtttgttagaataactttaactctttaagtactgatt-gcaatttgcagGTCATCTGTTGGGTTCTGGGGGAATACGGAACAGCAGATGGAAAGTATTCTGCTTCTTATATCAGTGGGAAGTTATGTGACATTGCAGAGGCATATTCCA

upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G08320.1 (Glycine max), 3'ss of exon 6
--------------------gtagt-tatttttcttgtccttt--ctattccaaactatagttttgggatgttttaagttgattcattatgtt-----cagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                    ||  | |||||  |   |  |||  || ||| | |    || | ||   | |||||   | |||| |  |  |     ||| |||| || |||||  | ||||||||||| || || ||||||||| |||| ||||| ||||| | ||||||  | |||||||| ||||||||  |    |
gtactttctatcccttttatgttttatatttccccacttgttttacttttcaagaagccagatctg---tcttttagcataattcgtagtactgattacagGTAATCTGTTGGGTTCTTGGGGAATATGGCACTGCTGATGGAAAATATTCTGCTTCGTATATCACTGGGAAGCTATGTGATGTTGCAGAGGCATATTCAA

upper sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------gtagttatttttct---tgtcctttctattc-caaactatagttttgggatgttttaagttgattcattatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                               ||  ||  ||||||   |||      ||||| ||||       |||   || ||    |||| ||| | || | ||| | || || ||||| ||||| || |||||||| || | ||||||  |||| ||||| ||||| | ||| || || ||||||||||||||||||||    |
gtacattctgttctatctggacactatttttgtcatttgttttctgcatgtaggcattattcacaaaactcttgtttattatcttagttgttggttc-tgatctacagGTTATTTGTTGGGTTTTGGGTGAGTATGGAACTGCGGGTGGAAAGTATTCTGCTTCCTATATCACTGGAAAGTTATGTGATGTGGCAGAGGCCCATTCAA

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: 46 (upstream exon), 49 (downstream exon)
Score: 88

GTAGATTCTTATGTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCTTTCCTTCAGgtagttattt ... ttatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 82

GTAGATTCTTATGTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCTTTCCTTCAGgtagttattt ... ttatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

GTAGATTCTTATGTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCTTTCCTTCAGgtagttattt ... ttatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 40

GTAGATTCTTATGTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCTTTCCTTCAGgtagttattt ... ttatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctattccaaactatagttttgggatgttttaagttgattcattatgttcagATAATATGCTGGGTGTTGGGGGAATATGGAACAGCAGATGGAAAACATTCGGCTTCTTATATTATTGGGAAATTGTGTGATGTGGCAGAGGCCCACCTCA
                                   agttgat  putative branch site (score: 40)
               tatagtttt  TA-rich tract