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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgatgatgaaattgccatagataagatatgtatataactgaaattaaaaatggctgtactttcctaacatttgctgttttgctcacctgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG

Basic information

species Zea mays
transcript GRMZM2G030144_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 17
--tactgatgatgaaattg--ccatagataagatatgtatataactgaaattaaaaatggctgtactttcctaacatttgctgttttgctcacctgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG
  | |      | | ||       ||| |    |  |||  |     | ||  |||||    |    ||    | ||||  | | |     |  ||  |||||||| |||||||||||||||||||| || ||||||| ||| |||||||||||||||||||  || ||||||||||||||||||||||| || ||||| ||||
aattccatcattcagatgagtttgtagtttgctttagtagttgtgaaacatacaaaatactcgaggctt----atatttcatttctgctgaatttggatttcagTTTATCCAGTTGCGTTTGGACCCCGCTAGCAGCAACACGCTTCCTGCCAGTGGAAATGATTCTGTTACACAAAGCCTCAGTGTCACAAATAACCAACATG
















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|91876800|gb|EB406757.1|EB406757
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|113701558|gb|EE679062.1|EE679062
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGTACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|60345980|gb|DN212953.1|DN212953
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|71433259|gb|DR814309.1|DR814309
EST:     TAGCAACCACTACATTCACAGATTTCGTTTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|213178150|gb|FM186361.1|FM186361
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|67021834|gb|CO450583.1|CO450583
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTGGGACCCANCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|91876799|gb|EB406756.1|EB406756
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT
EST: gi|88751809|gb|DY535950.1|DY535950
EST:     TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAG                         TTCATCCAGTTGCGTTTGGACCCAGCGAGCAACAACACTCTTCCTGCCAGT
genomic: TAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGT

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), 46 (downstream exon)
Score: 34

ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 46

ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45

ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 44

ACAACCTGGAAAACCTCAGGAGACTACAATTAGTGCTTCTTTCACAAATTTAGCAACCACTACATTCACAGATTTCGTCTTCCAGGCAGCTGTGCCAAAGgtagcatttg ... tgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaaaatggctgtactttcctaacatttgctgttttgctcacctgtgtttcagTTCATCCAGTTGCGTTTGGACCCAGCGAGCAGCAGCACTCTTCCTGCCAGTGGAAATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATG
                                       ctcacct  CT-rich tract
                      taacattt  TA-rich tract