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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacaacaacaaaataggcttcttttgtgaaattcttgttatttctctcctttgactcacacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG

Basic information

species Arabidopsis thaliana
transcript AT2G30970.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 8
-----gtaactacaacaacaaaataggcttcttttgtgaaatt--cttgttatttctctcctttgact--cacacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
     ||     ||    | |   ||  |  | ||    | |   | |  ||||  | |   ||   |     | | | | | | | |  ||  |  ||||||||||||||||||||||||||| | ||||| |||||||| || |||||||| |  ||||| || || || ||||||||||| ||| | || ||
gttatgttcactcagtctctatggagattgatattccacattcagcctaatattattgttagttatatggtgaatattaaaaacgtaagcgtatttgcagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAGGTGGATCGCTTAACCAATGAATACCATATTTACATGACCCGTAATGGCAGAATAAG

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 8
gtaactacaacaacaaaataggctt--cttttgtgaaattct-------tgttatttctctcctttgactcacacagtcatatctttatggtgata---acagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
||||||  | |||  ||| |   |   ||||  ||  | | |       | ||| ||||    ||  | | |  ||   ||||  || || |  |    |||||||||||||||||||||||||||  | ||||| ||||| || || ||||| ||||  || |  || ||||| ||||| |||||||| || || ||
gtaact-tagcaatcaaacaaattatgctttgatgggaatttagcataatattagttctgaaattgtaataatgcaaaaatattcttttgattttgtggacagATTGGAATGTTCTGCTACAGTGGTATGACACCTGAACAAGTCGATCGCTTGACAAAAGAGTTCCATATCTACATGACTCGTAACGGGCGGATAAG

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 8
--gtaactacaacaa--------caaaataggcttcttttgtgaaattcttgttatttctctcctttgactcacacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
  ||   |  ||||         |      |  ||   || ||    | ||  ||| |       |||  || |  |   |    |  ||     || ||||||||||||||||||||||||||| | ||||| ||||| |||||||| |||||||  ||||| ||||| || |||||||| || ||  | || ||
atgtccttgaaacatgtcctttccggtgcggatttacgttttgtgcgtattagtatgtggtgaacttgtatctctgaacaaagggtacatctctgta-cagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 8
-gtaactacaacaacaaaataggcttcttttgtgaaattcttgttatttctctcctttgactca--------cacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
  |  | ||| || ||  |||  |  || |      |||  ||  || ||      ||| ||          | ||  | | ||||| |  |     |||||||| ||||||||||||||||| || ||||| ||||||||||| ||  | |||| ||| | ||| || || |||||||||||||| ||||||||
acttccaacatcatcatcatacccaactgtccaagtattggtgccatgtccaagtattggctagttgcttttctcacacttttctttgttatttgtgcagATTGGTATGTTCTGCTACAGTGGATTGACACCTGAACAGGTTGATCGTATGACAAACGAGTTTCATATTTACATGACCCGTAACGGTCGTATCAG

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 8
gtaac-tacaacaacaaaataggcttcttttgtgaaattcttgttatttc----tctcctttgactcacacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
|||   || ||      |||    || ||||    | || || |  ||||    | || |   |  |  |||| | |  ||   |  ||  |||||||||| ||||||||||||||||| || ||||| ||||||||||| ||  | ||||  |||| ||| ||||| ||||| || || || || |||||
gtattgtagaatttgtcaatttatttgttttactcatttattttcctttccacatttcttcaaatgcttacagaccttgctgattcttgcaaacagATTGGCATGTTCTGCTACAGTGGTTTGACACCTGAACAGGTTGATCGAATGACAAATGAATTTCATATCTACATGACTCGCAATGGTCGCATCAG

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|86044665|gb|DR340420.1|DR340420
EST:     GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAG                         ATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
genomic: GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAGgtaactacaa ... gtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
EST: gi|86044680|gb|DR340435.1|DR340435
EST:     GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAG                         ATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
genomic: GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAGgtaactacaa ... gtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
EST: gi|86079557|gb|DR375314.1|DR375314
EST:     GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAG                         ATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
genomic: GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAGgtaactacaa ... gtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
EST: gi|86044669|gb|DR340424.1|DR340424
EST:     GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAG                         ATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
genomic: GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAGgtaactacaa ... gtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA
EST: gi|125257296|gb|EL271381.1|EL271381
EST:     GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAG                         ATTGGAATGTTCTGCTACAGTGGGTTAACACCAGGACAGGTTGACCGCTTA
genomic: GCCTTGAGAAGTTAGGATCGCCTTTGTCATGGGAGCACGTTACCAAACAGgtaactacaa ... gtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgttatttctctcctttgactcacacagtcatatctttatggtgataacagATTGGAATGTTCTGCTACAGTGGGTTAACACCAGAACAGGTTGACCGCTTAACAAGCGAATATCACATCTATATGACCCGTAACGGCCGTATCAG
                     gactcac  putative branch site (score: 2)
                                  atatctttat  TA-rich tract