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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcatttatagattatgcagcagactatgtcattttattgtacattacatgtgtcagactcatcagtgagttacaacatctgctgattgcttgttggacccattattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
gtatgtgcatttatagattatgcagcagactatgtcattttattgtacattacatgtgtcagactcatcagtgagttacaacatct---gctgattgcttgttggacccattattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG
      | |  | |||  | |||||  || |   ||       |||||||   ||   | | | |  |   ||| |||| |  | |    |||  |||||||||| |  ||| |||  ||||| ||||||||||||||||| || ||||||||||||||||| || || || ||||||||||   | |||||||| || |||||||
------gtaagtctag--tgtgcagaggatttgctc-------tgtacatattatagattacattt-tggatgaattacgatctttattactgggtgcttgttggtcttattcttg--cagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG

upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtgcatttatagattatgcagcagactatgtcattttattgtacattacatgtgtcagactcatcagtgagttacaacatctgctgattgcttgttggacccattattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG
   |   |||||||    |     |   | ||| || || |||  ||  || | ||  |||   | |    |  ||||  | | ||| ||  |  || ||||           || || | || ||||| || ||||| ||||||||||||||||| ||||| |||||| | |||||||   |||| ||||| || || ||||
-cttaaacatttatctcatccttggagaagtatttctttatatcttatgttcc-tggatcatgtttac---tttgttatga-aactg-tgtctagtttttgg-----------tgtagGTTGAAAAACAAGAGTTTGGGCTTAAGCCAATGAATTGCCCAGGGCACTGTTTGATGTTTGAACATAGAGTTCGTTCATATAGAG
















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|67033102|gb|CO461851.1|CO461851
EST:     AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG                         ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
genomic: AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
EST: gi|87157710|gb|DY402499.1|DY402499
EST:     AAACTTCTGGACACGCCGCANACTATAAGGAGAACATGTTTGTTTTTGAG                         ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
genomic: AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
EST: gi|32940354|gb|CF045173.1|CF045173
EST:     AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG                         ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
genomic: AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
EST: gi|211197538|gb|FL314132.1|FL314132
EST:     AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAG                         ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT
genomic: AAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGT

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: 47 (upstream exon), 47 (downstream exon)
Score: 349

GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 205

GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 210

GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 196

GTGTTGAGCCCAAATATTTACAATATGCAACTATGGGAAACTTCTGGACACGCCGCAAACTATAAGGAGAACATGTTTGTTTTTGAGgtatgtgcat ... tattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatcagtgagttacaacatctgctgattgcttgttggacccattattgtgcagATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG
                      tgctgat  putative branch site (score: 196)
                                           attattgt  TA-rich tract