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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttgacactttaactttgaatgtatgtttttttaaattgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 5
gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttgacactttaactttgaatgtatgtttttttaaattgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC
|||||  |   ||||    ||     ||  | |        |||    | |  | ||  |   |   ||| ||  | ||    || | ||||  | ||| |||||||||||||||| ||||||||||||||  ||||||||||||||||||| ||||| || ||| ||||||| |||||||||||||| |||||||| ||||
gtatgttagttgtgtactcctaagccaaagtcaataaaatgtccccaatatattattgaatgat---actgtgcttatac---ttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 5
gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttgacactttaactttgaatgtatgtttttttaaattgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC
|||||  |   ||||    ||     ||  | |        |||    | |  | ||  |   |   ||| ||  | ||    || | ||||  | ||| |||||||||||||||| ||||||||||||||  ||||||||||||||||||| ||||| || ||| ||||||| |||||||||||||| |||||||| ||||
gtatgttagttgtgtacccctaagccaaagtcaataaaatgtccccaatatattattgaatgat---actgtgcttatac---ttataaaatcatcattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 5
--------------------gtatgcgataggtgttaatcttgattaagattat-cttttactccattttgttgtgtttgacactttaactt--tgaatgtatgttt--ttttaaat---tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC
                    || ||  | |  | | |||    ||||||||||| ||| |   |  || | | ||  |    | || |||||  |||    || |||    | ||||   | |  || |||||||||| ||||| ||||||||||| ||| |||| || ||| |||||||||| ||||| ||| | ||||| |||||||||||||| |||||||||||||
gtactctattgctcttcattgt-tgttacacatatcaattaacattaagattatacttattgactcttatatggttatgcttaattcaacttcatgagctcatatttggcatgaaatccttctcgttcagGGTCTTGGAAAAACCCTTCAAACTATATCACTGCTTGGATATTTGCATGAGTTTAGAGGAATAACCGGTCCCCACATGGTTGTTGCACCAAAGTCCACTC

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttga-cactttaactttgaat-----gtatgtttttttaaattgttattt--------agGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC
               | || ||  ||   || | | | |  |   | ||||| | | | | || ||||  |||||       | || |  |   || ||| ||||         ||||||| || |||||| | ||||| ||||| ||  |||| |||||||||||||| ||||| ||| ||||||| |||||||||||||| ||||| || ||||
---------------tgatttttttttctat-aacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC

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|32838474|gb|CD978152.1|CD978152
EST:     TTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG                         GGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAG
genomic: TTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATGgtatgcgata ... tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAG




















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: 361

GCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATGgtatgcgata ... tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

GCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATGgtatgcgata ... tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 52

GCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATGgtatgcgata ... tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATGgtatgcgata ... tgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtgtttgacactttaactttgaatgtatgtttttttaaattgttatttagGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC
               ctttaac  putative branch site (score: 94)
                tttaactttgaatgta  TA-rich tract