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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgtttttatcgtattatctagattggtttttgaattgtttgcaatcatatgaacattgatagaataatactttcccatgtttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG

Basic information

species Arabidopsis thaliana
transcript AT5G20000.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 2
-gtatga-atgtttttatcgtattatctagattggtttttgaattg--tttgcaatcatatgaacattgatagaataatactttcccatgt-----ttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG
  | ||  |  || | ||    || | |       ||||  ||| |   |   ||   | ||   |    |   || | ||||  | || |     ||||||| |||||||| || || ||||| || |||||||| ||||| || || || || ||  |||| || ||||| ||||||||||| || |||||||||||| 
gatctgtcacattgtcatttggttctgttagccctttttgtaatggaaatcctaaatttctgtttaccagtgctatta-acttctcaatataattattcagGTACATCCAGAAGGCAAATATGTGGTGGATATTGATAAAAGCATTGATATTACAAAGATCACACCTTCAACAAGAGTTGCTCTTCGAAATGATAGCTATA

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 2
gtatg-aatgtttttatcgtattatctagat-----tggtttttgaattgtttgcaatcatatgaacattgata--gaataatactttcccatgtttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG
 |||| |||||||   ||  |  |   |  |     |  ||  | ||       |||    | || || |  |   || |  | |||| |  |  ||||||| || ||||| || || ||||| || ||||||||||||||||| ||||| || ||  | |||||||| || |||||||| || || || || || ||||
ttatgcaatgtttagttctgaaaacacacgtcatcctaattaataaaacaggatcaaaaccaagatcaattgtgctgatttttcctttactcttcttcagGTCCACCCAGAAGGAAAATATGTCGTTGATATTGACAAAAGTATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTTCGCAACGACAGTTATG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 2
--gtatgaatgtttttatcgtattatctagattggt--ttttgaattgtttgcaatcatat----gaacattgatagaataatactttcccatgtttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG
   | |  |   |||| |  ||      |  ||     | |||   ||| || |||   |     ||  |||      |||||| |||||    ||| ||||||||||||| |||||||||||||| |||||||| || |  |||||||| || ||  |||| || |||||  |||||||||| || ||||| |||||||
atttctctaccattttcttttacggctgaatttaacaatgttgtgatgtatgaaatgtgagttcagatgatttggctgataatattttccttctttttagGTTCATCCAGAAGGGAAGTATGTTGTTGATATTGATAAGAACATAGACATCACTAAGATCACACCTTCAACCCGAGTTGCTCTTCGCAATGACAGCTATG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 2
-------gtatgaatgt-ttttatcgtattatctag--attggtttttgaattgtttgcaatcatatgaacattgatagaataatactttcccatgt-ttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG
       || ||  |   |||| | | |     |||  |   || | ||  ||  |||   |||| |  |   | ||  |    | |||| || ||| ||||||| |||||||| |||||||||||||| ||||||||||| |  ||||| || || ||  |||| |||||||| ||||||||| | || |||||||||||||
gttgtctgtgtgggtacattttgtagaacccgatagcaaacagtgtatggttttcttgtc-tcatttctatggttattcacc--ttcttttccttgtgttcagGTACATCCAGAAGGGAAGTATGTTGTAGATATTGACAAGAACATAGATATCACAAAGATCACACCATCAACTAGAGTTGCTTTACGGAATGATAGCTATG

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|164134587|gb|ES030839.1|ES030839
EST:     ATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTT
genomic: ATGTGGGTGAAGTGGTAAAAGTGATGGGAAAAAACAAGGTCTTGGTTAAGgtatgaatgt ... catgtttcagGTTCATCCAGAGGGGAAGTATGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattgtttgcaatcatatgaacattgatagaataatactttcccatgtttcagGTTCATCCAGAGGGGAAGTATGTTGTCGATATTGACAAAAGTATAGACATAACGAAACTCACTCCATCAACGAGAGTTGCTCTCCGTAATGATAGCTATG
                       cattgat  putative branch site (score: 4)
                                       ctttcccatgtttc  putative PPT
                        attgatagaataata  TA-rich tract