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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgtataacataattgcatcactggccctggcatttgctgttatattaaccatttaccctttccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG

Basic information

species Zea mays
transcript AC235544.1_FGT004
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235544.1_FGT004 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 4
gtatgctgtataacataat-tgcatcactggccctggcatttgctgttatattaaccatttaccctttccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG
||| |   | | ||||||| |  || |  | |  ||  ||||||  |||  |||||  | | || ||||  ||||||||||||||||| ||||||| ||||||| |||||| ||||||||| |||| ||||||||||| |||||||||||||| || |||||||||||||||
gtaagtcatttgacataatctttattatggcctttgtaatttgcaattaatttaactgtatgccttttc-gattgaagTTTACCTGTTATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCAG

upper sequence: AC235544.1_FGT004 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtatgctgtataaca--taattgcatcactggccct-ggcatttgctgttata-ttaaccatttaccc---tttccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG
                 |||||||   |  ||  ||||        | ||  |   | ||      | ||  | || |||  ||    ||| |  || ||| || || ||  | |||| | | ||||| ||||| | | | |||   |||||  |  ||   ||||||||||||||||| ||||||||||||| |
gtgagcttttatttcttgtatgctacttgccaactaatatttgttttagctgtcaaccttgagaaatgtaactcactattgccctgttttttcgcttaaagATTGCCAGTCATTCAAGCACTGGCTGCAGAAGTTAGGCAAACAACCCAATCTCTTCTTCATCAGCTTCTCCAGAAACTTCGATCAAATATTCTG
















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|148931304|gb|EC874156.2|EC874156
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
EST: gi|211510351|gb|FL119756.1|FL119756
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTCAAGAAGACAGTACAA
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAA
EST: gi|71770990|gb|DR968927.1|DR968927
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
EST: gi|211232015|gb|FL402276.1|FL402276
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTCAAGAAGACAGTACAATC
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
EST: gi|149040625|gb|EE046866.2|EE046866
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
EST: gi|71312838|gb|DR792945.1|DR792945
EST:     GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGA                         TTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC
genomic: GCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATC

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: 46 (upstream exon), 48 (downstream exon)
Score: 74

GTGTATACGGAATGGGAACTATGATGAAGCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 33

GTGTATACGGAATGGGAACTATGATGAAGCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 24

GTGTATACGGAATGGGAACTATGATGAAGCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 67

GTGTATACGGAATGGGAACTATGATGAAGCACTTGATCTAGAAGCTTTTGTGAGCAAAATATCGAAGTTGCACCCAGAgtatgctgta ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactggccctggcatttgctgttatattaaccatttaccctttccaattgaagTTTACCTGTTGTCCAAGGATTAGCTGCTGAAGTAAAGAAGACAGTACAATCATTAATTTCCCAGCTTCTCCAGAAACTCCGATCAAATATTCAG
                          tattaac  putative branch site (score: 67)
                                ccatttaccctttcc  CT-rich tract
                       ttatattaaccattta  TA-rich tract