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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

Basic information

species Zea mays
transcript GRMZM2G006428_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttga-gcaaaa-atatccaatattgacttcg--aaactgtctatt---catggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG
         || | | ||  ||  ||| |     || ||| |  || |||   ||||   || ||   | |  |||  |   |||| ||| ||    ||||||||||||| || |||||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| || |||||||||||||||
-------gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG

upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
------tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG
      |  |  | |     |||| |||   || |  |  ||| |      | |||   | |     | ||||  | | ||  |   ||  | |      |||||||||| |||||||||| ||||||||||| || || |||||||| || |||||||| || || || ||||| ||||||||||| || ||||| |||||||||
agaatctatttgtgcaggattctttatggtttactataactatgtttaattttttt---ccatttgttgcaatgctaaatttta---tgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG

upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggttt----cagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG
      | | |      | ||    |   | || | |||| |      |    ||    |     ||||||  |||     | | |||  ||  |||    |||||| || || ||    || || ||||||||||| ||  |||| || ||||| ||||| || ||||||||||| || ||||| ||||| ||||||||||||
-aaatatgcgttcgagctgatattctgtcg-acttttttcttagagaataactcatcctttattcatattgtgttccc--ttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG

upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 7
tggtctttcctctctcttaatgcaataatgcacat--atttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG
 || |    |   |||||||  ||   ||  |     || |  ||    |    ||    ||||  ||        |   | ||   | ||| | |   |||||| || || ||    || ||||| ||||| || ||| |||| ||||| ||||| || || |||||||| ||||| ||||||||||| ||||||  ||||
-ggaccaaaccaactcttaagtcatagatttaggacaatgtgatgaagttccttgcctttatatttaacgcattagtgttatctcctttttctttgag-cagGATTCTTGCAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAG

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|76281609|gb|DV021177.1|DV021177
EST:     GTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTG                         GATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGNNNN
genomic: GTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTGgtatagaagg ... atggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAA




















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: 213

TGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTGgtatagaagg ... atggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 154

TGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTGgtatagaagg ... atggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 97

TGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTGgtatagaagg ... atggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

TGCACCGAGGAAGCTCATCGTCCAGTAGACTGTGCCACTGTTTCGAAGTGGATCCTCAAGAACAGTGCGGAGTCGGAGAATATGAACTGgtatagaagg ... atggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG
                     tattgac  putative branch site (score: 149)
         aaaaatatccaatatt  TA-rich tract