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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA

Basic information

species Arabidopsis thaliana
transcript AT1G63700.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
  |||||  |        ||| |||  |   |  |   | ||  |||  ||   ||  | |   |    |        || ||  | |  ||| ||   ||  ||||| ||||| ||||| ||||| ||||||||  |||||||||| || ||||| || ||| |||||||||| ||||||||||||||  |||||||  | || || || |
-gaagttgcatgatagcatctaggatttcattaatgagttat-ttatgtaccacttttgattttcttttt--------tggcttcacttattatttgtgcc--ccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
  |  || | |||| ||||   | || |  || ||   ||  |||    |||   || | | |    |       | || |||| |  || | | ||       |||  ||||| ||||| || || |||||||| ||||||||||| || ||||| || ||| ||||||| || || |||||||| |||||||||||   ||| || || |
ccacattctgcaga-attttacgaacttcacttttgcttg-cactcctgact-cctctgtttactttaa------aaataactatacactatccatttatt---caaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
gtaagttttacagatatttcttggacatttctgttctctgatactat-caactgtttcagctcaaccaagtcatgcacatgactagattc-tttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
        || |   |  |  |     ||||||      |  | ||   |  |  ||   | ||  ||  |  || |     ||| || | | | | |        |||   |||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||  |||| ||||| |||||||||||||| ||||||||  | |||||| | |
--------tagaatcacattct-----tttctggatggagggagtacatagttacttttccccatgcatcttgtg-attcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
gtaagttttacagatatttcttggacatttctgttctctgatactat-caactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
           |||  |   ||   | ||| ||  |      | ||   |  | |||   ||||  ||  |  ||   ||    |     | | | |         ||  ||||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||  |||| ||||| ||||||||||| || ||||||||  | |||||||| |
----------tagaattgcatt---cttttttggacggaaggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
gtaagttttacagatatttcttggacatttc-tgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttacttt----cccctcccaat--tcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
                  | || || ||||     |||   | | ||  || | ||| ||   |      | || |  | || |   ||   |  |||    | | |   |||   ||||| |||||||| || ||||||||  ||||||||||||| ||||| || ||||||||  | |||||| ||||||| ||  || |||| | ||  |||||||
------------------ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgt-tgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 7
gtaagttttacagatatttcttggacatttc-tgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttacttt----cccctcccaat--tcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
                  | || || |||      |||   | | ||  || | ||| ||   |      | || |    || |   ||   |  ||       | |   |||   ||||| ||||| || || ||||||||  ||||||||||||| ||||| || ||||||||  | |||||| ||||||| ||  || |||| | ||  |||||||
------------------ttttagaaattcgacaatctactaaaatactaaatatttaagagaagatgt-tgatacttcagattgtttttagtgattcatggttctttataataaacagGTAGATGATAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
      |     ||  |||| |   |||| |  || | | | |  |  |  ||     | |  |           |  |||     | |||  || |   |    ||  ||||| |||||||| || || ||||||  ||| ||||| |  |||||||| || ||||||||||||||||||||||| || |||||||| |  || |||| ||
------tcctttgaagtttcatctgcattac-attatattagatcactagatggc---gattgattcttcagcttatgtgaaattttccttggctatattccttgaa--cagGTGGATGACAAACTCTACATATATTCGGAATATGTATATGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGTTTGGTGAAATAGCTATTCATA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
      |     ||   ||| |   |||| |  |    |   ||  |  |  |     | |    ||  | |||    |||     | |||  || |   |    ||  ||||| |||||||| || || |||||| |||| ||||| || |||||||| || ||||||||||||||||||||||| ||  ||||||| |  || |||||||
------tcctttgaagcttcatctgcattacattatattagaacactagatggcgattgattcttcagcttatg----tgaaattttccttggctatattccttgaa--cagGTGGATGACAAACTCTACATATATTTGGAATATGTATCTGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGCTTGGTGAAATAGCTATTCGTA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S44_113V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gtaagttttacagatatttc----ttggacatttctgttctctgatacta--tcaactgtttcagctcaaccaagtcatgcacat---gactagatt-ctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
       | ||   |||   |  |||     ||  ||||  |   | ||  ||  ||  || | | ||   | |       |     ||  |   ||   || | | |   |     || |     ||| | || || | | ||||||||||| |||||||||| || || || || ||| ||||||| || |||||||||||    ||    |||   |   | || |
gtgcgacgcaaaccttatgcaccttttaatatttaacatgacgtctgtcacatgttaactccattattcttgttgctttggggtcgacatgtcgggatctgactgcgtcgttgggatcttctgg--cagTTGGAAGATAGGTTGTATATATATTTGGAGTATGTTTCTGGAGGATCAATCCATAAACTGCTCCAAGAGTATGGCGCTTTCAAAGAGCCAGTGGTGCGCA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S8_299V6.1 (Physcomitrella patens), 3'ss of exon 6
-------gtaagtttt-acagatatttcttggacatttctgttctctgatactatca--actgttt--cagctc----aaccaagtcatgcacat--gactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
       | ||  ||| | || | ||  ||     | |   |    |  || | | |  | |||||  | |||     ||   | || | |||||  ||| |  ||  ||   ||          |  || | || |||| | ||||||||||| | |||| |||||| ||||| || ||| ||||||| || |||||||||||    |||   ||    |   | || |
gtaccacgaaatctttgatagcttttgattcatagtgtgactggagtagtattgtgatgagtgttttgcggctgtggaaattgaatcgtccacatttgacgatgttgcttgggttt--------gtgtagTTGGAGGACAGGTTGTATATATATTTAGAGTTTGTCTCAGGTGGATCAATCCATAAACTACTCCAAGAGTATGGCGCTTTTAAAGAACCGGTTGTACGCA

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|124888880|gb|EH967782.1|EH967782
EST:     TAAGCCGTTTACGACACCAAAATATAGTGCAGTATTATGGCTCTGAAACC                         GTCGATGACAAG
genomic: TAAGCCGTTTACGACACCAAAATATAGTGCAGTATTATGGCTCTGAAACCgtaagtttta ... cccaattcagGTCGATGACAAG
EST: gi|164069464|gb|ES199850.1|ES199850
EST:     GTATTATGGCTCTGAAACC                         GTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATC
genomic: GTATTATGGCTCTGAAACCgtaagtttta ... cccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
                             ttctttactttcccct  CT-rich tract
                            attcttta  TA-rich tract