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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtg----accctttgattcccttcccttttcatagttt--tcgattggcggttagattgtcttgctgactgtctttttgagctctgcag
| |||| |||||| ||||||||||| || |||||||||||||| ||| | ||| ||| | | || || | | | || | | ||| | | ||| | | | |||
GAAAGTACAAGCCAGTGATCAAGAAGGCTATGGTGGAACTTGACGgtacgaagcacttctattatcaacgctaacagtaatgtgatttatggacctttacccaaaatctcatttcatctatcatccattttcag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 7
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgt-----gaccctttga---ttcccttcccttttcatagttttcgattggcggtt-agattgtcttgctgac-tgtctttttgagctctgcag---------
| ||||||||||| ||||||||||| || ||||||||||| || ||| || | || || || || || | || | | || |||| | | | || | | ||| | || | ||||
GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTGGAACTCGATGgtacgatgaactttggaatgtttgatttactgctgattatgatgtttttatggtttatgtccttttcccaaaatgtgatattatgtgctgcccgatttccag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgac---tgtctttttgagctctgcag-----------------------
| ||||||||||| ||||||||||| || ||||| |||||||| ||| | | || || | | ||| | || | | || |||| || |||| |||| | |
GCAAGTTCAAGCCAGTGATCAAGAAGGCTATGGTCGAACTTGATGgta--tgatgaactctggaatgttcgcttgatttactgatgatcatgacgtt-tcttaatggttcatgtcctttttccatgtctgatatcctgtgacgccaatttccag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgatt-ggcggttagattgtcttgctgactgtctttttgagctctgcag------------------
|||| |||||||||||||||||||| ||||||||||||||||||||| | | | | | | | ||||| | ||| | | | | | ||| |||| | || || |
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAACTTGAAGgtaaacatatatattcatgaaaacttcattgatttgggctcaataatccactaacgctactg--tgtcactcagaaaaatgaaatgaaagggagggtaaaat

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag--------------------
|||| |||||||||||||||||||| ||||||||||| ||||||||| | || | | | | || | ||| | | | | | || | || | | | | |||
GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatgtattcatctattgtttgctctgcaaaattagtga--gaactatatttttcacccgcatggaaggata-gcaatgaaatgaaggggagggaaa

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgatt-----ggcggttagattgtcttgctgactgtctttttgagctctgcag------------
|||| |||||||| ||||||||||||||||||||||| ||||||||| | | | | | | | |||| ||||| | | | | || | | | ||| |||| | | | |
GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAGgtaaacatatatattcatgaaaacctcattgttttgggctccatagtccactaacgtagcaagtgaactacactttttacccatattgagccacaaaaat

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 12
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtg-accctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagc-tctgcag---------------
|||| ||||| |||||||||||||| ||||||||||| ||||||||| | | || | | | ||| | | || || || | | | | | ||| | ||
GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAGgtatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatattcttctattgtctgcttacaaaattagtgagaacta

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag----------------------------------------------------------------------------------------------------------
||||||||||||||||||||||||| |||||||| |||||||| ||| | | ||| | | | | | | |||| | | || ||| || | || | ||| | || || |
GTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATGgtaagaagt--atttctatgcatgcttgtcatttt--gtctccatttgtattaactcgtagaattgcttct--agtcctagaaacatgcagcaaatagtcatttgctattaccccatattcatttgtttcacttgtgaatggttgtcgccccaaccaaatatgactaagcatacattttgaaatttcag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: EFJ12684 (Selaginella moellendorffii), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag
| ||| |||||| ||||| |||||||| |||||||||||||| ||||| | | | || ||| | | || | || | | | | | || | || | |
GCAAGAACAAGCCCGTGATAAAGAAAGCCATGGTGGAACTTGATGgtga---gtacaaacagttgacttgttgca-ttgacaatcgttgct--gctactcctcctcgcag------------------

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: EFJ13842 (Selaginella moellendorffii), 5'ss of exon 14
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag
| ||| |||||||||||| |||||||| |||||||||||||| ||||| | | | || ||| | | || | || | | | | | || || |
GCAAGAACAAGCCTGTGATAAAGAAAGCCATGGTGGAACTTGATGgtga---gtacaaacatttgacttgttgca-ttgacaatcgttgctgctact-cctcgcag----------------------

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|86088437|gb|DR384196.1|DR384196
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|86060419|gb|DR356176.1|DR356176
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|124796242|gb|EH885921.1|EH885921
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATT
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATT
EST: gi|86060418|gb|DR356175.1|DR356175
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|125269642|gb|EL283727.1|EL283727
EST:     TTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: TTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|124743697|gb|EH834859.1|EH834859
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCG
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCG
EST: gi|125297233|gb|EL311318.1|EL311318
EST:     GTAAGTTCAAGCCTGTGATCAAGTAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcag

- - - - - - - - - - AAGAAA
- - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - TTGAAG