Sequence
atgc intronic sequence ATGC exonic sequenceCGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53170.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttct-----ttgt-tactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag-------------
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TGTCAAAGGGTGTGATGACGCAAAGAAAGAACTCGAGGAGGTAGTTGAGTATCTAAAAAACCCTTCAAAGTTTACTCGGCTTGGTGGAAAACTACCGAAGgtaatttctatatgcaaattgcattctttgtgttccatatcatgct-ccgcggaatcttccagatacatatctgtgtgttctatattattattgattgaaatttcaaaagatgt-aaaccttgatgtttaatttgtctttttag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G156069_T01 (Zea mays), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctg----aaacatt--tctgaaatgtttgcctccag----------
|| || |||||||||||||||||| | || || || ||||||||||| |||||||| || || |||||||| || |||||||| |||||| | || |||||| ||| || || | | || | | | | | || || || | | | | || || | |||| ||| || || |||| |||| | ||||| |
TGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAGGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCCTTGGTGGAAAGCTACCTAAGgtaatcact--ctatgccatctcgcgagtaacatttatcgtcaccttgctccatgagttcctctatatatctgtcgcttttattggatgattgaactgttatgaatcttgctctgtaatgaattcctcctgtcctttgcag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G004040_T01 (Zea mays), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctac-taaagttagcattttgacctgaaacat-ttctgaaatgtttgcctccag----------------
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TGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAAGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCCTTGGTGGAAAGCTACCTAAGgtaatcact--ctgtggcaccctgcgagtaacattt----attgccaccttgctccatgagtttatctgttgtttttattggatggttgagctgttgtgaatcttgctctttaatgtattcctcttatacttttactttgcag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G08160.1 (Glycine max), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagac---tttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
|| || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| |||||||||||||||||||||||||| | | || ||||| | ||| || | | | || | ||| ||| | | | | | | || || | ||| || | | || |
TGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCCTTGGAGGAAAGTTGCCAAAGgtctgaagaggttaatttgtcatttttttttc-----ttttttttcctgagcttttttcatattcctattttctatgta-tagacttattcttatttcttggtagg----------------------
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA14G29780.1 (Glycine max), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagac---tttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
|| || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| |||||||||||||||||||||||||| | | || ||||| | ||| || || || | | ||| ||| | | | | || | || || | || ||| | | | || | | |
TGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCCTTGGAGGAAAGTTGCCAAAGgtctgaagaggttaatttgtcatttttttttcctga-----cagct------ttttttcatatttctattttccatata-tagacttcttattcttatttc-----ttagtaggaag-----------
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G13140.1 (Glycine max), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
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TGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCCTTGGAGGAAAGTTGCCGAAGgtctgaagaa-----gtaattgtatatttg-----------ttgaactttttttgc---tagtcagcacttgctta-tatttctgacctttttttttaaaaaaaatatggttggcttatc-----
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 6
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
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TGTGAAAGGCTGTGATGATGCAAAACAGGAGCTTGAGGAAGTAGTGGAGTACCTCAAAAACCCTGCAAAGTTTACTAGACTTGGGGGGAAATTGCCAAAGgtttgtaa----aaagacattttgttcttca-agtacataatc------ttattgcacaaaatggttatgcatatattctgctcaataccatgga-tgatggatctctctga-------------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|164091126|gb|ES182709.1|ES182709EST: AAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAG GGAATTCTTCTAACCGGGGCACCTGGTACTGGAAAGACATTGCTGGCCAAA
genomic: AAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactt ... ttgcctccagGGAATTCTTCTAACCGGGGCACCTGGTACTGGAAAGACATTGCTGGCCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCCTTGGAGGAAAGTTGCCAAAGgtatagactttctttgttactttgcatttgagaatatacaattgagaagtctttgcatttgattttctcccgtctactaaagttagcattttgacctgaaacatttctgaaatgtttgcctccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA