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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttatacaaagagctctttcttctagtcgatgatatcagcatgtcgttacaggtacctgtgtttccagcctcacgcatgcttgtctggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG

Basic information

species Zea mays
transcript GRMZM2G022308_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022308_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g30880.1 (Oryza sativa), 3'ss of exon 7
gtatcttatacaaagagctctttcttctagtcgatgatatcagcatgtcgttacag-gtacctgtgtttccagcctcacgcatgcttgtctggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG
||||    | |||  |  | |||||| |                |  |  |||||| |||  | || | | |  || | ||    |||| |   || |||||| ||||||||||| ||||||||||||||||||||||||||  | |||||||| ||| |||| || |||||| ||    | |||||  ||||||| || |
gtatgcatttcaataacttttttcttgt---------------tacatttttacagtgtatttctgctcctactctaatgc---tttgtat---attccagGTTAATCCACAGTTTTACGCATTCAGATGGATCACCTTGCTATTGACGCAGGAATTCAAGTTTCGCGACTGCATCCATATATGGGATGCACTGTTAGGTG

upper sequence: GRMZM2G022308_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S8_313V6.1 (Physcomitrella patens), 3'ss of exon 8
-----gtatcttatacaaagagctctttcttctagtcgatgatatcagcatgtcgttacaggtacctgtgtttccagcctcacgcatgcttgtctggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG
      ||  | | |    |    ||| ||  |||  | |    || |  |    ||| ||     |||| ||   |  | |       || | || |  | |||||||| || || |||||||| ||||||||||| || |||||||||||||| |||||| | ||   ||| |  ||  | || |||||| | ||  |  |  
cacggatacttgaaatcgtgtttgcttgctcttagaagttctgttctgtgtacttttatagaa---tgtggttgaggattaaattgcctttatgtgtc--cacagGTCAACCCCCAATTCTACGCTTTCAGATGGATAACTTTGCTGCTAACGCAAGAGTTCAACTTTGCTGATTCTCTTCGACTTTGGGACTCTCTTCTCAGTA
















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|166500756|gb|EG235816.1|EG235816
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTCTACGCATTCAGATGGA
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGA
EST: gi|50326619|gb|CO521745.1|CO521745
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTTTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
EST: gi|16917540|gb|BM073331.1|BM073331
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
EST: gi|211055806|gb|FL456006.1|FL456006
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTCTACGCATTCAGATGGATCACCTNTNGCT-STAACGC
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCT-T-GCTGCTAACGC
EST: gi|76918970|gb|DV167536.1|DV167536
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
EST: gi|71758907|gb|DR956844.1|DR956844
EST:     TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAG                         GTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG
genomic: TGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAG

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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 2

CAACAGCGTGGTTGGCATACGCTCCACAATTACTACACTATCACAGCTTCTGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG


Block sizes: 36 (upstream exon), 14 (downstream exon)
Score: 1

CAACAGCGTGGTTGGCATACGCTCCACAATTACTACACTATCACAGCTTCTGAGAAGACACGACGAGGAACTCTGGCGGCATTTAGAAGTTGTAACCAAGgtatcttata ... ggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgttacaggtacctgtgtttccagcctcacgcatgcttgtctggcatcccagGTCAATCCACAGTTCTACGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCG
                          gcctcac  putative branch site (score: 1)