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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

Basic information

species Arabidopsis thaliana
transcript AT1G64650.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 4
gtgaatctcttacctt-accttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaat--cagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
||  || | | |  |  ||| | |     | |||| |||  | | |   |  ||     | | ||     |  ||     || || | ||||  ||||||| ||||| ||||| || || ||||| ||||| |||||||| || || |||||||| ||||| || || ||||||||||||||||||||||| || ||
gtagatttatcatgtccaccatagcaaagggcataatgtttttt-taaatatttttttttattttaacatatcaaatggtttcttttgaaatttcagATGAAAAGATTGCATTGCTTGGAGCTATACAGTCACTGTTTGAGGGTTCAATGTACACTTTTGTTTTCCTGTGGACTCCTGCTTTGAGCCCAAATGATGA

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
||     |    | |  | |  |  |  | ||||    ||||||  | ||   || |  ||   |||| |       || ||| ||    |||||||| ||||| |||||||| || || || |||||  ||||||| || ||||||||||| ||||| || || |||||||| || ||||| ||||| |||||
gtatgcttaacccatctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatct--tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 4
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccag---ctttattcttccactaaccaccttt-ttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
  | ||   ||| |    ||          || |     | || | | ||| |       ||  |||  |   |||||  | |    |      |||||||| ||||| |||||||| || || || |||||  ||||||| || || |||||||| ||||| || || |||||||| || ||||||||||| |||||
--gtatgctttagcccgtctcatcagaacgcagagaaccaaatatttatgcatatgaaacctgcatttgttttctaacatcgtccactggatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCGATGTACACATTTGTCTTCCTATGGACTCCAGCGTTGAGCCCAAATGAAGA

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
||     |    | |  | |  |  |  | ||||    ||||||  | ||   || |  ||   |||  |       || ||| ||    |||||||| ||||| |||||||| || || || |||||  ||||||| || ||||||||||| ||||| || || |||||||| || ||||| ||||| |||||
gtatgcttaacccatctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatct--tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------gtgaatctcttaccttaccttg-gtttttgacatactgtaatat-gtctttgcttccagctttattcttccactaacc---------acctttttattaaat---cagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
                                                                    ||||  | | |  |||   || | |  |    |||||  ||   |  ||||    ||||   | |    ||| |  |         |   | | | | |||   ||||||||||||| ||  |  | ||||| || |||||| ||||||| || ||||||||||| |||||||| |||||||| || || |||||||| |||||  |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------gtgaatctcttaccttaccttggtttttgacatact--gtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
                                                                                               | | |    |||  | | || |||    ||  | |  ||   ||||      |   |  | |  ||| ||| |      ||||  ||| |  ||||||||||||| || ||  | ||||| || ||||| ||||||||||| |||||||| || ||||| || || ||||| || || |||||||| |||||  |
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtct-ccattg--tgtctttggattga--cagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA

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|164132509|gb|ES084792.1|ES084792
EST:     AGTTCAAGAACGCTGCATCTGCCATTGCTTCTG                         ATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCA
genomic: AGTTCAAGAACGCTGCATCTGCCATTGCTTCTGgtgaatctct ... attaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCA
EST: gi|86062547|gb|DR358304.1|DR358304
EST:     CAAAGACCTTCTTACCCAGTTCAAGAACGCTGCATCTGCCATTGCTTCTG                         ATGAGAAGATCGCTTTGCTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCA
genomic: CAAAGACCTTCTTACCCAGTTCAAGAACGCTGCATCTGCCATTGCTTCTGgtgaatctct ... attaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCA
EST: gi|86062546|gb|DR358303.1|DR358303
EST:     CAAAGACCTTCTTACCCAGTTCAAGAACGCTGCATCTGCCATTGCTTCTG                         ATGAGAAGATCGC-TTCGCTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCC
genomic: CAAAGACCTTCTTACCCAGTTCAAGAACGCTGCATCTGCCATTGCTTCTGgtgaatctct ... attaaatcagATGAGAAGATCGCATTA-CTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
                             cactaac  putative branch site (score: 1)
                                      cctttttatt  putative PPT
                                        tttttattaaatca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA