Sequence
atgc intronic sequence ATGC exonic sequenceTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34660.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
||| || || | |||| |||||| |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| |||||||||||||| ||||| ||| || ||| |||| | || | || | | ||| ||| || || || | ||||| || | | | || || | | | |
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgt---------gatttcactatg----tattacactattgcataatgagttta--cctttaccttttgt-----ctttgtatctctttattaacaagggggcatattcattgt-cactttt--------------
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttatt-attcgcatgatagaactttacttatgcgcctgctttaatccaaacag
||| || ||| | | || |||||| |||||||||| ||||||||||| | || || || ||| | || ||||||||||| |||||||||||||| ||||| | | || || | | |||| | | | | | ||||| | | | ||| || || ||| ||| || | |
TGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcgatatgtatttcacta--ttgcataataagtttacatttaccttttgttttgtatctctttatcaacaagagatggtatccattgtcacttttg----------------------------------
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: AC199567.3_FGT002 (Zea mays), 5'ss of exon 1
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
|||||| |||||||||| |||||||||||| || || || ||| | || ||||||||||| |||||||||||||| ||||| ||| || ||| |||| | || | || | | ||| ||| || || || | ||||| || | | | | || | | | |
-------------------ATGGTTATGGGAGCTCCTTTGGAGGATGCTCACCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgt---------gatttcactatg----tattacactattgcataatgagttta--cctttaccttttgt-----ctttgtatctctttattaacaagggggcatatccattgt-cactttt--------------
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G11950.3 (Glycine max), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaac----tttacttatgcgcctgctttaat-ccaaacag-------------------------------
||| ||||||||| |||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| |||||| | | || || | | | || | | | | || | | || |||| | | | | | | | | | | | | || | || | | ||| | |||| | |
TGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTAGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCGGAAGCCCAGgtat--tcgagtatt-tatctttcatttaacttttcaaaacttgttggacatcctttttcatttgtcacctgctttttgtagtctgtcttctgtgtttcagtgcatgtttcattaatgattttattttactattttgtggtgtaattactctgtcttttgaacctagacag
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G04210.1 (Glycine max), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataa-taccatgaagctatttaattaccgttag---------------tagaatatgggttttttcc-tcttccaagaactagt---cattttattattcgcatgatagaact--ttacttatgcgcctgcttt--------aatccaaacag
||| ||||||||| |||||||||| ||||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||||||||| ||||| | || || | ||| | || || || ||| | | | || |||| || ||||| | ||| ||| |||| | | || | | || || || | || | || | | | ||
TGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCCAGgtgttctagaatttatctttcatttaacttttcaaaacttgttggacatcctttttcatttgtcacctgctttttgtctgtcttctgtgtttcagtgcatgtttcattaatgattttattttattattttgttgtgtaattactctgtcttttgaacctagatag
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G01120.1 (Glycine max), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagata------ataccatgaagctatttaatt--accgttagtagaatatgggttttttcctcttccaagaactagtcattttatta-----ttcgcatgatagaactttac--ttatgcgcctgctttaatccaaacag
||| ||||| ||| | |||||||| |||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||| ||||| |||||| ||| || || || || ||| || || | || || || | | || | || |||| || | || | | ||||| ||| | || || | | ||||
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgtatctggaattttatctttcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactatttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacag
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G01100.2 (Glycine max), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaag--ataataccatgaa-----gctatttaattaccgttagtagaata--tgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
||| ||||| || | |||||||| |||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||| ||||| |||||| ||| || ||| | | | | |||| || | ||| || | | || || || ||| | ||| || ||| ||| |||| ||| | || || | | ||||
TGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCACAGgtatctggaattttattgtacttttttcatttgtcacctgcttacattttgggaaatgtctgaatgagtatctgtttcatcaacga-----tttttttttcctatgt--actttttaattacactgtcttttaaacctagacag
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G01120.2 (Glycine max), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagata------ataccatgaagctatttaatta--ccgttagtagaatatgggttttttcctcttccaagaactagtcattttatta-----ttcgcatgatagaactttac--ttatgcgcctgctttaatccaaacag------------------------
||| ||||| ||| | |||||||| |||||||||||||||||||||| | |||||||||||||| |||||||||||||| || ||||| ||||| |||||| ||| || || || || ||| || || | || || || | | || | || |||| || | || | | ||||| ||| | || || | | ||||
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgtatctggaattttatctttcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactatttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacaggctattgaagtttccaaacgccag
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctct---tccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
||| ||||||||| | || ||||| ||||||||||||||||||||||| |||||||||||||||||||||| |||||||| ||||||||||||||||||||| | ||| ||| || || | || || | |||| |||| | | || || | | | || || || | ||| ||
TGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTCAGgtattcttaaa--caattttatttagtttttcaaatg------------tatgcacttttctcctagggtttgagtcatatttgatattttcttttattgctgagtttttgttt------------------------
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 5'ss of exon 5
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
|| || || ||| | |||||||| |||||||||| |||||||||||| |||||||||||||||| ||||| |||||||| |||||||||||||||||| || | | || | || | || | || | | || | | || || | | |||| | | | || ||| | | ||| |
TGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTCAGgtaacgttagatatgagacattt---ctttatatctgcagtctgctggatgcatcttccatttcttaccaaaatttgagcgattcatt-tcattgtcatattcc-------------------------------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|47831064|gb|CK120748.1|CK120748EST: GACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAG GCTACAGAAGTTGCCAGACGCCAAGCAAAGGCGAGAGAGTCTCAAGGTAAT
genomic: GACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaa ... atccaaacagGCTACAGAAGTTGCCAGACGCCAAGCAAAGGCGAGAGAGTCTCAAGGTAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA