Sequence
atgc intronic sequence ATGC exonic sequencegtacgaactaattgtaatcgaaaaaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
-----------gtac-gaact----aattgtaatcgaaaaaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttt--tccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
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aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatag---ttaacat-gtaatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
-----------gtac-gaact----aattgtaatcgaaaaaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttt-tccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
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aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatag---ttaacatgtattttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g50260.1 (Oryza sativa), 3'ss of exon 3
--------------gtacgaactaattgtaatcgaaa--aaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
||| ||| | | | || | || ||| | | || | || | | | || | |||||| | | ||| || |||||| |||| || || || || ||| | | | | || |||||||| ||||||||||||||||| |||||||||||| | || || |
ttcagtgctcacttgtagaaaccgacaggattcaggactaagggaaagctaaaaacactagta-caagtatctgaagtaatatttgctctctgtgatgc-agGCGATGATTGTGTTTCCATCCAGACAGGCTGCAGTGACATAAACATACATAATGTGAACTGTGGACCAGGGCATGGGATCAGCATTGGTGGTCTAGGAAG
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 5
---gtacgaactaattgtaatcgaaaaaatc-----gttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttt------tccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
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cctgtaaaccctgcatgtcaaaggacatgtttcagagttaagagtacactgaaaaactgctgtaaactagcataacattcctttgtcctattcgatgcagGTGATGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACACAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 5
-------------------gtacgaactaattgtaatcgaaaaaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
| || | || | || | | | |||||| | | | || ||| |||||| || ||| | | | |||| |||||||| || || || || || || ||| ||| | || | || || ||||||||||||||||| |||||||||||||| ||| | || ||
catgtatactctgcacttcaaaggacatgtttcagagttaagactacactgaaaaactgctgtgga--gtatcataacatcgtt--ttgtcctat-tcgatgcagGTGACGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACATAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
---gtacgaactaattgtaatcgaaaaaatcgttata-aaact------cgtaaata--tcgggt---cttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
| | || || | | | |||| | | || | ||| | ||||| | || || ||||| || | || | | |||| | |||||| || ||||||||||| ||||| || ||||| || | ||||| |||||||| || ||||||||||||||||||||||||||||| || || || ||
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgc-agGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
upper sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
---gtacgaactaattgtaatcgaaaaaatcgttata-aaact------cgtaaata--tcgggt---cttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
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tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgc-agGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAAMapped 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|124951701|gb|EL027043.1|EL027043EST: TCTTCAGAACACCAGAGATGTCATGATTCACACCACCACACTAGCTTGCG GAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGT
genomic: TCTTCAGAACACCAGAGATGTCATGATTCACACCACCACACTAGCTTGCGgtacgaacta ... gtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
ttgatttccctctgtt CT-rich tract
tcttaatat 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaactaattgtaatcgaaaaaatcgttataaaactcgtaaatatcgggtcttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA