Sequence
atgc intronic sequence ATGC exonic sequencegtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 3
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgt-tgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
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-----------------------------------------------gtaggttttgtcctggtaccagatt-gtgggttcacattagatgtgtttcattatttattgtcaagttaat-gctgtattatggccat---gcagACCTTCAACTTGATGTTAAAGGTTGTCGTGATGTGTATGCATCGTTTGATAAATATGTTGAAGTTGAGCGCCTCGAAGGTGATAATAAGTATCATGCAGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 7
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
|| ||| ||| || ||| | || || ||| | || | ||| | |||||| ||| || ||||| || ||||| ||||| ||||| || | ||||||||||| || ||||| || ||||| ||||| || ||||| || || || |||||||||||||||||
--------------------------------------------------------gtaagctttttcacattgaacattcagtatcattt---ttaatttagtgc-------ttact--catgttataacatt---gcagATCTACAGCTTGATGTCAAAGGTTGTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 7
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtctt--attctatttatacaat-tgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
|| | || | | ||| ||| | || || | |||| || | | | | || || || || || | || | | | | | | || | | || | || | | ||||||||||| || || ||||| ||||| ||| |||||||||||||||||||||||||||||| |||||||||||||||||||| || |||| ||| || || ||
--gtattcatttttggt-tcaagcttacattctttgtagctaggcattcgctattaatgggaatgcatgatacttgaactatatatgtcctaatataaaaagaaaggaaaaaaaatgaactgcatttttatttttgcatggcagACCTACAACTTGATGTAAAAGGATGCCGGGATGTTTATGCTTCTTTTGACAAGTATGTAGAAGTTGAACGTCTTGAAGGTGATAACAGATACCAAGCTGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaac-tttattgtcatgttctaatcttatgg-cagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
|| | ||| | | | | |||| | || | | ||| || || | |||| | | || | | |||| | |||| | ||||||||||| ||||| ||||||||||| |||| ||||||||||||||||||||||| ||||| | || || || |||||||| || || ||
------------------------------------------gacgtgcgca-tgaaccttttccaggtggaagtacagctccaattcggcactagattgtaagcattcagcgtttaatattatagtatgttcttcttttcagATTTGCAGCTGGATGTGAAAGGATGCAAGGATGTATATGAATCTTTTGACAAGTATGTTGAAGTAGAACGGTTGGAGGGCGAGAACAAATACCACGCCGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
| | ||| | | || | || || | | || | || || || | || | ||||| || || | ||||| | ||||| ||||| ||||| |||||||||||||||| ||||||||||||||||| || || ||||| | ||||| || ||||| ||||| |||||
--------------------------------------tgtgggcatatcccttc--tcgtgatagtaggataattgggaatcttcttgatgctttgagc-attgcgaattgtttatgtgtatctttggtgtactttgcagATTTGCAGCTTGATGTGAAAGGGTGCAAGGATGTTTATGAATCTTTTGACAAGTATGTCGAGGTAGAACGCTTGGAAGGCGAGAACAAGTATCACGCAGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 5
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
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------------------------------------------------------------------------------gtttgtttctgcattttcgggaatttcaggcaatattgttaacccgttggaa-----taacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATAAGTACGTCGAGGTAGAGAAGCTCGAAGGGGATAACAAGTATCACGCTGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 5
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacac-caactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
|| |||| | || || || ||| || || | ||| || | |||| | ||||| ||||| ||||||||||||||||||||||| || ||||| || || || || || || || ||||| || ||||| |||||||| ||
------------------------------------------------------------------------------gtttgtttctgc-attttcgggaattgcaggcaatattgttaacccgttggaa-----taacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATAAATACGTCGAGGTAGAGAAGCTCGAAGGGGATAACAAGTATCATGCTGA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 7
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatct-tatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
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----------------------------------------------------------------------------------------------gtatgttgatat-tgagtagtctgggcttctcacaacgtgtgttacagATTTGCAATTGGATGTCAAGGGCTGCAAGGACGTGTATGCGTCATTTGACAAGTATGTGGAGGTTGAGAAACTTGAGGGGGATAATAAGTACCATGCCGAMapped 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|125082103|gb|EL143084.1|EL143084EST: TGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAATCATTTTACG ACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTT
genomic: TGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAATCATTTTACGgtatagtaat ... cttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
ttctaat putative branch site (score: 2)
ttattctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagtaatatacattatcactctttgtcttattctatttctacatttgcactcggttgtcttattctatttatacaattgcactctgttgtcttattctatcacaccaactttattgtcatgttctaatcttatggcagACCTTCAGCTGGATGTTAAAGGCTGCAAGGATGTTTATGCTTCTTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGAGACAACAAATATCATGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA