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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgttttccttgtcctatctattccagattatagtttcgggatattatatgttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA

Basic information

species Zea mays
transcript GRMZM2G146697_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g68750.1 (Oryza sativa), 3'ss of exon 7
---------gtagttgttttccttgtcctatc-tattccagattatagtttcgg-gatattatatgttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
          |      ||| ||| |  |||| || |||  |  ||  |||| | | ||   ||||||||||||||  |  ||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||| ||| ||||||||||||||||||||  |
gtgattttaatttcctgttttcttcttatatcatactccgtaccatgttttctgtggtagattatgttgattcattctactttcagATAATATGCTGGGTTTTGGGAGAATATGGAACAGCAGATGGGAAATATTCAGCTTCATATATTATTGGGAAGCTGTATGATGTGGCAGAGGCCCACCCAA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 6
-----------------------------------gtagttgttttc-cttgtcctatctattccagattatagtttcgggatattatatgttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                                    ||  | |   | |||||  || || ||| ||     || |  |   | |   ||  |   |  |   |  | ||| |||| || |||||| ||||||||||||| ||||| |||||||| ||||| ||||| ||||| | ||||||| | |||||||| ||||||||  |    |
gtagtttctaactttctatcctttttttttatgttttatatttccccacttgtttta-cttttcaaggagtcagatctgtcttttagcataatatgtagtactaattacagGTAATCTGTTGGGTTCTGGGGGAATATGGCACAGCTGATGGAAAGTATTCTGCTTCCTATATCACTGGGAAGCTATGTGATGTTGCAGAGGCATATTCAA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G35240.1 (Glycine max), 3'ss of exon 6
-------------------------gtagttgttttccttgtcctatctattccagatt-atagtttcgggatattatatgttgattcatttcatgtt-----cagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                         | | ||    | ||  |  ||        | ||| | ||| |  | | | || |  || | ||  |   | ||     ||| | || || |||||| |||||||||||||||||| ||||||||| ||||| ||||| ||||| | ||||||||| |||||  | ||||||||  |   ||
gtactttctatcccacttatgctttggattttcccttctcattttactccgaagaaattgaaagtgtttgtagaata-actttaactctctaagtattgattgcagGTCATCTGTTGGGTTCTGGGGGAATATGGAACAGTAGATGGAAAGTATTCTGCTTCCTATATCAGTGGGAAGTTATGTGACATTGCAGAGGCATATTCCA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA01G35650.1 (Glycine max), 3'ss of exon 6
-------------------------gtagttgttttccttgtcctatctattccagattata---gttt--cgggata---ttatatgttga----ttcatttcatgtt-cagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                         | | ||    | || ||  ||        | |||| |   ||||    | |||   |||  | || |     | ||| ||  || ||| | || || |||||| |||||||||| ||||||||||||||||| ||||| ||||||||||| | ||||||||| |||||  | ||||||||  |   ||
gtactttatatcccacttatgctttggattttaccttctcgttttactctgaagaaattaaatgtgtttgttagaataactttaactctttaagtactgattgcaatttgcagGTCATCTGTTGGGTTCTGGGGGAATACGGAACAGCAGATGGAAAGTATTCTGCTTCTTATATCAGTGGGAAGTTATGTGACATTGCAGAGGCATATTCCA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G08320.1 (Glycine max), 3'ss of exon 6
-----------------------gtagttgttttc-cttgtcctatctattccagattatagtttcgggatattatatgttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                        ||  | |   | |||||  || || ||| |||    || |  |   | |   ||  |   |  |      | ||| |||| || |||||| | ||||||||||| || || |||||||||||||| ||||| ||||| | ||||||| | |||||||| ||||||||  |    |
gtactttctatcccttttatgttttatatttccccacttgtttta-cttttcaagaagccagatctgtcttttagcataattcgtagtactgattacagGTAATCTGTTGGGTTCTTGGGGAATATGGCACTGCTGATGGAAAATATTCTGCTTCGTATATCACTGGGAAGCTATGTGATGTTGCAGAGGCATATTCAA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagttgttttccttgtcctatctattc-cagattatagtttcgggatattatatgttgattc----------atttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
   |||| |||  || ||  |||| | | || |  ||  |||   |  |  |  | ||| |||           ||| |  ||||| | || |  ||||||||||| |||||||| ||||| ||||| |||||||| || || ||||||| ||| ||| |||| ||||||||||| ||  ||   |
---gttgattttgttctctgatctctccgcataccatttttttccgcaacgaatttttgtttcttactattgggtttaaacttcagGTCATTTCTTGGGTTTTGGGAGAATATGGCACAGCTGATGGGAAATATTCTGCCTCCTATATTAGTGGAAAGCTGTGCGATGTGGCAGATGCATACTCAA

upper sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gtagttgttttccttgtcctatctattccag-attat------agtttcgggatattatat--gttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                        || || | |   ||||  | |  ||    | |||||      |  |   |  |||||| |  |||| |   | | || | ||| | || || ||||||||||| || |||||||| || | |||||| ||||| ||||| ||||| | ||| ||||| ||||||||||||||||||||    |
gtacattctgttctatctggacactatttttgtcatttgttttctgcatgtaggcattattcacaaaactcttgtttattatcttagttgttggttctgatctacagGTTATTTGTTGGGTTTTGGGTGAGTATGGAACTGCGGGTGGAAAGTATTCTGCTTCCTATATCACTGGAAAGTTATGTGATGTGGCAGAGGCCCATTCAA

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|89762346|gb|DY689972.1|DY689972
EST:     CATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAG                         ATAATATGCTGGGTTTTGGGGGAATATGGAACAGC
genomic: CATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGC
EST: gi|9952284|gb|BE638867.1|BE638867
EST:     CATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAG                         ATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCA
genomic: CATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 152

GTGGATTCATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

GTGGATTCATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 142

GTGGATTCATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 121

GTGGATTCATATCTCCGCATTGTCGGAGAGCCAAAGCTTCCTTCTTCGTTTCTGCAGgtagttgttt ... tcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctattccagattatagtttcgggatattatatgttgattcatttcatgttcagATAATATGCTGGGTTTTGGGGGAATATGGAACAGCAGATGGAAAATATTCAGCTTCTTATATTATTGGGAAGTTGTGTGATGTGGCAGAGGCCCACCTCA
                                 tgttgat  putative branch site (score: 121)
                                       ttcatttc  CT-rich tract
                         atattatatgttgatt  TA-rich tract