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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtttatttattccactcgttcgacctgacagaatttcatggcttctgtattctcactgtatggttatggatatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG

Basic information

species Zea mays
transcript GRMZM2G110309_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 7
gtatagtttatttattccactcgttcgacctgacagaatttcatggcttctgtattctcactgtatggttatggatatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG
   ||   |  ||| | ||||| || ||||| |||   ||||||   |||||| |||| |||||||   | |        |  || ||||||||||| |||||||| || ||||| ||||| |||||||| || || ||||||||||||
--gtatgctgcttacttcactcatttgaccttacat--tttcataatttctgt-ttcttactgtatttctgt--------ttcagATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG

upper sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 11
---------------------------gtatagtttatttattccactcgttcgacctgacagaatttcatggcttctgtattctcactgtatggttatggatatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG
                           |     ||||||||||   |   | |    |||||  ||       | | | |||  |  |  | ||| | |||| |||    |||||||| |||||||||||||| || ||||||||||| ||||| || || || || ||| | |||
atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgaca--atc------cctttatatagtttccttttgggtgtggaaatc----agGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
















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|32920556|gb|CF025368.1|CF025368
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT
EST: gi|32796142|gb|CD948378.1|CD948378
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTA
EST: gi|211166794|gb|FK981048.1|FK981048
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
EST: gi|16925516|gb|BM078584.1|BM078584
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
EST: gi|32796753|gb|CD948989.1|CD948989
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTA
EST: gi|71768291|gb|DR966228.1|DR966228
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
EST: gi|32789721|gb|CD941957.1|CD941957
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTA
EST: gi|14245205|gb|BG873787.1|BG873787
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTA
EST: gi|32799039|gb|CD951275.1|CD951275
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGACGTTA
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTA
EST: gi|32921260|gb|CF026072.1|CF026072
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT
EST: gi|32921005|gb|CF025817.1|CF025817
EST:     GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAG                         GTGGTGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT
genomic: GCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGT

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: 44 (upstream exon), 45 (downstream exon)
Score: 14

AGAGGTCACCAGAGCAGGGGCAACGCAGAATCAGGCGCCCGTTCTCTGTTGCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

AGAGGTCACCAGAGCAGGGGCAACGCAGAATCAGGCGCCCGTTCTCTGTTGCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

AGAGGTCACCAGAGCAGGGGCAACGCAGAATCAGGCGCCCGTTCTCTGTTGCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

AGAGGTCACCAGAGCAGGGGCAACGCAGAATCAGGCGCCCGTTCTCTGTTGCTGAAGTAGAAGCACTTGTGCTCGCAGTCGAAAAGCTTGGAACCGGAAGgtatagttta ... tatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacagaatttcatggcttctgtattctcactgtatggttatggatatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG
                        ttctcac  putative branch site (score: 57)
      aatttcat  TA-rich tract