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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatcatttcgagctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA

Basic information

species Arabidopsis thaliana
transcript AT5G01020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g02830.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------acatcatttcg-agctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgac-tcta-atactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
                                                                    |||||    |   | | | ||| |      |   |||  | || |   ||   |  ||   |   |  |   | |  |||  | || ||||  ||     ||| |||||||| || ||||||||||| ||||||||||| ||||| ||||| ||  | ||||| ||  | || ||  | || ||| || | || ||||  ||
gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagttt--ctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA

upper sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------acatcattt--cgagctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgac-tcta-atactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
                                                                                |  | ||||  | |     | ||| |  |   |   |||  | || |   ||   |  ||   |   |  |   | |  |||  | || ||||  ||     ||| |||||||| || ||||||||||| ||||||||||| ||||| ||||| ||  | ||||| ||  | || ||  | || ||| || | || || |  ||
gtactgtcctcgttttatcttttttaaattttctacatttttttctgagtagcgttgttacccttcatcaaaatgtgaccaggttatttgtcaaaaagaaaagtttaccaagtaatatgcaagtatgcagttt--ctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGTAGGGA

upper sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
-acatcatttcgagctacatagtctctctt-tttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
 |  |    |  || |      | |||| |  ||     |||   |||   |  | |    |    | |      ||  ||    | ||   ||||  | ||| ||| |||| ||||| || ||||| ||||||||||||||||||||||||||| ||||||| ||||| || ||||| || |||||  |||||||||| ||
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatga-aatgtgc-agGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA

upper sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 5
acatcatttcgagctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
                       |   ||     |  |  | ||    || ||   ||    || | || |  | | |  || |  |     | | | ||| |||||||| ||||| || ||||| |||||||||||||||||  | || |||||| | || || |||  |||  |||| ||| | ||||| |     ||
----------------------gtaagttcacaaagaaagaaaaaaaatt-gagagttcttgaacttaaaaggatcgtacctttgtt-----tcctccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGCGA

upper sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 5
acatcatttcgagctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
                       |   ||        |  | ||   ||| ||   ||    || | || |  | | |  || |  |     | | | ||| |||||||| ||||| || ||||| |||||||||||||||||  | || |||||| | || || |||  |||  |||| ||| | ||||| |    |||
----------------------gtaagttcacaaggaaagaaaaaaactt-gagagttcttgaacttaaaaggatcgtacctttgtt-----tcctccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGAGA

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|125310239|gb|EL324324.1|EL324324
EST:     TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTG                         GACACTTGACGGCC
genomic: TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctg ... aatgcactagGACACTTGACGGCC
EST: gi|47829930|gb|CK119614.1|CK119614
EST:     TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTG                         GACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctg ... aatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG
EST: gi|47830578|gb|CK120262.1|CK120262
EST:     TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTG                         GACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctg ... aatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG
EST: gi|86072121|gb|DR367878.1|DR367878
EST:     TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTG                         GACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTTCTA
genomic: TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctg ... aatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTT-CTA
EST: gi|116406702|gb|EG449294.1|EG449294
EST:     TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTG                         GACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctg ... aatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA
                                         tactaat  putative branch site (score: 1)
          attacacaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcatttcgagctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - -ctacata
- - - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - - -acaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actctaa