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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA

Basic information

species Arabidopsis thaliana
transcript AT5G36880.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G36880.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G157269_T01 (Zea mays), 3'ss of exon 6
----------------------------------------gtaactgcagagcaacttaataattgtcaaaatt-ccttcattgtttttttttttcgaatggttc--taa--aagtcttctgtgggtgg-tggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
                                           |||    || |  |   | |||   |||||  |||||       || | | ||   ||  ||  |||  || |  | | ||  ||   | |||| | |  |||||||| |  || | |  |||||    || || |||||||||||||||||||| ||||| |||||| |  | ||||| ||||| || || || |||||||
gtatgccaagatcaaaattgcaacatactttctgcgtgcacggactctgcagaacttctgtgattcataaaataaccttccaaacccttctgtatcagctgtatcactaatcaatttatttctgaatgaacgatgatgaat--agGATGTTGTGCCTGATTTCCCAACTAAATGCGATGTGGAATGGGTTGATGCAGAGGATCCACTGTTTCTTTTGTACACAAGTGGCAGCACAGGAAAGCCAA

upper sequence: AT5G36880.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0068g00640.t01 (Vitis vinifera), 3'ss of exon 6
--gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcg--aatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
  |||     |  |||| || |||||  |  || |      | ||   ||  |       ||| ||  |   ||   |   ||  |        ||  |  |||||||| || || ||||||||||  | ||||| ||||| |||||||||||||||||||| || ||| ||||||| || ||||| || || || ||||| |
aagtatagaaatggcaa-ttgataatc-ttgaattgaaggaagtgccgttaataaagagcaatagtattttgaggaattgatgattaacaactgtc-ttccagGATGTTGTTCCTAAATATCCAACTACTTGTGATGTGGAGTGGGTTGATGCAGAAGATCCACTTTTTCTGCTCTATACAAGTGGGAGCACGGGAAAGCCCA

upper sequence: AT5G36880.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S398_15V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
                                            |   |    ||  |    |   |||  || |||     ||| |     || || |||| |    | ||| ||        |     || ||   | ||||| |  |  |   |||| ||| |   ||||| ||||| |||||||| ||||||||| | ||||||||| | |||||||||||||| ||||||||||| |
gttgagtttgtctgtttccctcttgttctctgtgtttttgatgatcctttgttagagaggcgagtgttgctaacattttgaaattttcgacgttgtttgaattg---gataagactgacacctctc-caatgttcctatcagGATATCGTGCCATCATATGCAAAAGAATGTGATGTGGAGTGGGTTGACGCAGAAGATACGCTGTTTTTGTTATACACCAGTGGAAGCACTGGGAAGCCCA

upper sequence: AT5G36880.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ18689 (Selaginella moellendorffii), 3'ss of exon 6
gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
                    || |||     ||  ||    | | | |||||||     || |||       | ||    ||            | ||||||||  || |  | ||||| ||    |||   ||||||||||| || || || |||||  |||||||||| ||||||||||| || |||||||| ||||
-------------------gtatttg-----atctctctggtctctcttttttttatcgggctct------ttgcttcacgt-----------ttctagGATGTCGTTCCAAATTATCCCACTGATTGTCCAGTGGAATGGGTAGACGCGGAGGATCCTTTGTTTTTGCTGTACACCAGTGGCAGCACTGGGAAACCAA

upper sequence: AT5G36880.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ36126 (Selaginella moellendorffii), 3'ss of exon 6
gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
                                 |  || ||   | |  | | ||   |  || | |  |   ||| ||  |   | |      | ||||||||  || |  | ||||| ||    |||   ||||||||||| || || || |||||  |||||||||| ||||||||||| || |||||||| ||||
--------------------------------gtatttgatctctctggtctctc---tcttttttatcgggctctttgcttcacgtt------tctagGATGTCGTTCCAAATTATCCCACTGATTGTCCAGTGGAATGGGTAGACGCGGAGGATCCTTTGTTTTTGCTGTACACCAGTGGCAGCACTGGGAAACCAA

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|86060429|gb|DR356186.1|DR356186
EST:     CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAG                         GATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCA
genomic: CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAGgtaactgcag ... atcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCA
EST: gi|86060430|gb|DR356187.1|DR356187
EST:     CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAG                         GATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCA
genomic: CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAGgtaactgcag ... atcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCA
EST: gi|125046820|gb|EL119089.1|EL119089
EST:     CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAG                         GATGTTATTTCTCAATATCCAACATCGTGTGAGGTG
genomic: CAACAAGGGAAAACACTAAATGGCAGAATGGAAGAGATGTGTGGTGGCAGgtaactgcag ... atcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA
                 ttctaaa  putative branch site (score: 2)
                                              tcacttt  putative PPT
                 ttctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgcagagcaacttaataattgtcaaaattccttcattgtttttttttttcgaatggttctaaaagtcttctgtgggtggtggtgatcactttagGATGTTATTTCTCAATATCCAACATCGTGTGAGGTGGAATGGGTTGATGCAGAAGATCCCCTGTTTTTGCTCTACACCAGTGGAAGTACTGGGAAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG