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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaattttagtagcccccattgttttatgaccatgttggattttgagtgatttgatcttaaattgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

Basic information

species Arabidopsis thaliana
transcript AT5G58060.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
aattaattttagtagcccccattgtttta---tgaccatg-ttggattttgagtgatttgatcttaaat---tgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
       | |  | | ||   ||| |  |   || |  |  ||  |     | ||  |    | | |||   |  || || |||       | |   || | |  ||||||| ||||||||||| ||| |  |||||||||||||||| |||||||| ||||| |||||||| 
-------tcttcttgtccttgttggtccaaactgccagtacttaaacacgcactgcatcctgcatgaatgttttcttatgagataacttgatttcattattttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 3'ss of exon 3
-----aattaatt--ttagtagcccccattgttttatgaccatgttggattttgagtgatttgatcttaaattgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
      |||| ||  ||  ||     ||  | |  |   |     ||    |||  |  ||  |  |  ||||  | |||      | ||  |||  || ||| ||||| || ||||||||||| ||| || ||||||| |||||||| |||||||| || |||||||| |||
ggccatattattttcttgttaattgtcaacggtgcaccgcttaactgatgcttgtattgttaaacatctaatt--tcttgc-----ttcccaattattattctgcagGATCCTGCAGAGGCTGACAAGTTGCTGAAAATTCAGAGGGATTTGGATGAAACTAAGATTATTCTT

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------aattaatt--ttagtagcccccattgttttatgaccatgttggattttgagtgatttgatcttaaattgattttgggattgtcccgtatttgt--aatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
                                                               ||  ||||  | | ||  |   ||||| |||    |   |    |||| |   | ||     | | |  |        ||   | ||   |||  ||||||||||| || ||||||||||| ||| || ||||||| ||||| ||||||||||| ||||| || ||||||
gcatgtaaatacctcttttatgttgtatgagcttcagttagaggagttgttgatttttgtttgaaaaaattgttcaatattctaaattgtgttacattctgctaacctttttacacaattatgtatgactcaaacccc---tttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
---------------aattaattttagtagccc---ccattgttttat------gaccatgttggattttg--agtgatttgatcttaaattgattttggga--ttgtcccgtatttgt--aatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
                 || || ||    | |    | ||||||| ||       |   ||||  ||| ||  |    ||| |    |   ||| |        ||   | ||   |||  ||||||||||| || |||||||| || ||| || ||||||||||||| ||||||||||| || || || ||||||
gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgttacattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------aattaattttagtagcccccattgttttatgaccat--gttggattttgagtgatttg-atcttaaattgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
                                                                               ||   |||| | |        ||  ||| |    |   |||  |  |   || ||||  | |  ||| |  ||||     ||| |  | |||| ||||||||||| || || |||||||||||| |||||||||| ||||| ||||||||||| || || ||||| |||
gtatttctccacatttttctcattttgtttgttgcgtcataaggctgcatataggtacaattaattttttttgcatcataaactatttcaattttatttgttcctttcttcttaatggttcaagctatggtcatttataacccaaaatactttttattctgttc--tctttgaaatcttcagGATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT

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|124769523|gb|EH859653.1|EH859653
EST:     CTCCAATCTAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAG
genomic: CTCCAATC-AGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAG
EST: gi|125273313|gb|EL287398.1|EL287398
EST:     TCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAG
genomic: TCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAG
EST: gi|125041340|gb|EL113609.1|EL113609
EST:     ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGG
genomic: ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGG
EST: gi|164204950|gb|ES170588.1|ES170588
EST:     CTCCAATCAGCCTTGGCCATACTTAACCGAAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAG
genomic: CTCCAATCAGCCTTGGCCATACTTAACCG-AAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAG
EST: gi|86082551|gb|DR378310.1|DR378310
EST:     ACTCCAATCAGCNTTGGCCATACTTAACCGAAGCTTTAAGCAAATTTCAG                         GACCCAGCANAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAG
genomic: ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAG
EST: gi|125106561|gb|EL159950.1|EL159950
EST:     ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTT
genomic: ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTT
EST: gi|116387908|gb|EG430500.1|EG430500
EST:     ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAG
genomic: ACTCCAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAG
EST: gi|124964853|gb|EL039086.1|EL039086
EST:     CTCCTAATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAG                         GACCCAGCAGAGGCTGATAAGCTGTTGAAAAT
genomic: CTCC-AATCAGCCTTGGCCATACTTAACCGAAGCTTTAAACAAATTTCAGgttcttcact ... taatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtgatttgatcttaaattgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT
                 aattgat  putative branch site (score: 4)
                                                tcttc  putative PPT
      atttgatcttaaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaattttagtagcccccattgttttatgaccatgttggattttgagtgatttgatcttaaattgattttgggattgtcccgtatttgtaatcttcagGACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT