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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA

Basic information

species Arabidopsis thaliana
transcript AT3G54480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcg--tactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
 |     |||| ||    || |   ||   |  | ||   || ||  ||   |  |  | | |   | |    | ||| |  | ||  || |||   |||||||||||||||||| || |||||||||||||||||| | |  || || || || |||||  ||||| | ||||||||  |     |||   ||  |    |
-tgcttgattttgt-ccctgctaccatttattgcctgataatgtgacgctgtttatgtactttaaatgagctttttttagcatttcatttttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCATCCTCGACTGTGGTTGCGTGTTGAGAGGCCAATCAGAAATACAATAGA

upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009021_T01 (Zea mays), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA-------------------------------
                ||    | ||    |||| |||   |||     | |||    | | | |||||    || |            |||   |||||||||||||||||| || |||||||||||||||||| | |  || || || ||||||||  | ||||| ||||| ||  |     |||  |||       |                               
----------------ttaacatatactgctgacgtgg---tttaaaatgaactgttttttttatcaatttcattgt------------tgaacctgcagataggtataacaccgccctcgtttgccacagATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCT

upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgt--atctc-ttgt-gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
       || ||  || || |||| ||      | |   ||| |  |||  ||     |     | ||   | |||| | |  || || |||| ||   |||||||||||||||||| || |||||||||||||||||| | |  || || || ||||||||  | ||||| ||||| ||  |     |||  |||       |
---ctggatgtcacatgttttttg-atagcatgccttaacatatactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA

upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G21550.1 (Glycine max), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggca------tttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
  | |     |  |  | | ||   || |||  ||| |  |      ||  | || |||  |||    |||     || |           ||  ||||||||||||| | | ||| || || |||||||||||||||||||  ||  |||| ||||| |||||||||||||| || ||||| || |  || || || |||||| |
-cttaggcgctaatcctctcttaaaataattttctttgaaaaaataattaatagcatacagcagagcatttt----ctatcacaaa-gctgctattgagtttgcagATCGCTTTAATACCGCCCTCGTTTGCCACAGATGGAATTACTTGGCATGTCATCCTCGCTTGTGGCTTCGGGTTGATCGATCAGTTAAAGAGTTATCTGA

upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtac---tacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
   |   |||    ||  || |  |     |||     |   |||   | | |   ||   | |  | || | || | |  || ||  |   ||||||||||||| |||||||||| || ||||||||||||||||||   || ||||| |||||||| ||  | ||||| || || || || | ||| || |||| |||| |
--agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagt-ctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA

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|125065136|gb|EL132478.1|EL132478
EST:     TGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAG                         ATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGC
genomic: TGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAGgtaaaattgg ... gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGC
EST: gi|19874582|gb|AU235413.1|AU235413
EST:     CGACGATGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAG                         ATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTC
genomic: CGACGATGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAGgtaaaattgg ... gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
                 tttcaat  TA-rich tract