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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaagtgaattccatcaaaatgactattactagttgtcttgttcaaaatgtgacagacttgctcctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG

Basic information

species Arabidopsis thaliana
transcript AT1G64680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g02210.1 (Oryza sativa), 3'ss of exon 2
------gtaacaagtgaattccat-caaaatgactattactagttgtcttgttcaaaatgtgacagacttgctcctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
         || | | || |   | |    ||  | | |   |   |   ||  |||||     | || | |  || |      ||  ||||| ||||||||||| || || || |||||||| || || |||||||| ||||| || ||| | ||||||||||| ||||| || ||||| |||||||||
gtaagacggacgattcaactgtgttcgtcttggatttcaagcgagattcagtaaaaaattcagaaaacattcatctcc-----gtttcagGTACCTGGAGAACAGCGGCTGCGTCGGAATGTGCGTCAACATGTGCAAAATTCCGACGCAAAACTTCTTCACCAACGAGTTCGGACTCCCTCTCACCATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
gtaacaagtgaattccatcaaaatgactatt---actagtt---gtcttgttcaaaatgtgacagacttgctcctactg--ttgat-----------tgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
  | | |||   |    | ||| | |||  |   | || ||   | | |  | | ||| | ||    || |   |  |   |||||           |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||| ||||| || ||  | || |||
--agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 4
-gtaacaagtgaattccatcaaaatgactattactagttg----tcttgt-------tcaaaatgtgacagacttgctcctactgttgatt-----gaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
  || | |||   |    | ||| | |||   | || ||       ||||       |||| || |  |     |   | |  | || |||     ||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||| ||||| || ||  | || |||
aatagctagtatttattttgaaattcacttacattaattaaggccgttgtaacaatttcaacattttcccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 3
--------gtaacaagtgaattccatcaaaatgactattactagttgtcttgttcaaaatgtgacagacttg-ctcctactgttgattg--------aagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
          |  ||   |||| ||  | | |    || |     ||||    |   ||| |  |    ||  ||  | |||   | |         |||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||| || ||||||||||||||||| || || || || ||  | || |||
catatgtcacagtaaccaaatttcaatatattagaaataaaataatgtccaactactaatctttcttttttttctttttctgacaaattctcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAATTCCTACTCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S6_190V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------gtaacaagtgaattccatcaaaa-tgactattactagt-tgtct--tgttcaaaatgtgaca-----gacttgctc-ctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
                   ||   ||  |||| || |   ||  |||    | | ||||   ||||  | | |||  |     |||    |  || | | |||    || || || || || ||||| || || || ||||| || ||||||||||| || || ||||| ||||||||||||||||| || || || ||||| || |||
gtacttgccatttttttccactcttgttttccctctattctgcttatcttgaatctgtcaagtgttgtagaggtggtactaatgacacaatagctgcggatgagaacagATACCTAGAAAATAGTGGATGCGTCGGGATGTGCGTCAATATGTGCAAAATCCCGACCCAGGATTTCTTCACCAATGAATTCGGTCTTCCACTTACTATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ23359 (Selaginella moellendorffii), 3'ss of exon 4
gtaacaagtgaattccatcaaaatgactattactagttgtcttgttcaaaatgtgacagacttgctcctactgtt--gattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
                                   ||    ||  |  |||   || |     ||   ||    |  | ||  |||||||| ||||||||    ||||| |||||||| || |||||||| || ||||| ||||| ||||||||||| ||||| |||||  | || |||||||||
-----------------------------------gtgagatttctacaaagaagagaactaagcatgtaaaaatacgtttccagGTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG

upper sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
gtaacaagtgaattccatcaaaatgactattactagttgtcttgttcaaaatgtgacagacttgctcctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
                                  || | |||      ||  |    |  | || |   |||   | ||  |||||||| ||||||||    ||||| |||||||| || |||||||| || ||||| ||||| ||||||||||| ||||| |||||  | || |||||||||
-------------------------------gtgagatttctacaaagaagagaactaagcatg-taaaactac-gtttccagGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG

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|124943205|gb|EL019404.1|EL019404
EST:     TATCAAGAAATGCAG                         GTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGAT
genomic: TATCAAGAAATGCAGgtaacaagtg ... ttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGAT
EST: gi|125076355|gb|EL139539.1|EL139539
EST:     GAAGTGAATGGTGTGAAACAGAGAAGTGGAGTTCGTATCAAGAAATGCAG                         GTTATCTGGAGA
genomic: GAAGTGAATGGTGTGAAACAGAGAAGTGGAGTTCGTATCAAGAAATGCAGgtaacaagtg ... ttgattgaagGT-ATCTGGAGA
EST: gi|86083117|gb|DR378876.1|DR378876
EST:     TATCAAGAAATGCAG                         GTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGAT
genomic: TATCAAGAAATGCAGgtaacaagtg ... ttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactagttgtcttgttcaaaatgtgacagacttgctcctactgttgattgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
                                           tgttgat  putative branch site (score: 4)
                ttcaaaat  TA-rich tract