RetrogeneDB ID: | retro_cfam_1164 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 25:14958301..14958889(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000032664 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RER1 | ||
| Ensembl ID: | ENSCAFG00000019395 | ||
| Aliases: | None | ||
| Description: | RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30309] |
Retrocopy-Parental alignment summary:
>retro_cfam_1164
ATGTCCGAAGGTGACAGTGTTGGAGATTCTGTCCATGGGAAACCTTCTGTCGTGTACAGATTTTTCACGAGACTTGGACA
GATTTATCAGTCATGGCTAGACAAGTCCACACCTTACACAGCCGTGCGATAGGTAGTGACACTGGGCCTGAGCTTTGTCT
ACATGATTCGAGTTTACCTGCTACAGGGCTGGTACATTGTGACTTACGCCTTGGGAATCTACCACCTCAATCTTTTCATA
GCCTTTCTCTCTCCCAAAGTGGACCCTTCCCTGATGGAGGACTCAGATGACGGCCCCTCATTACCAACCAAACAGAATGA
GGAGTTCCGGCCCTTTATTCGAAGGCTTCCAGAGTTTAAATTTTGGCACGCGGCGACCAAGGGCATCCTCGTGGCCATGG
CCTGCACCTTCTTTGAGGCTTTCAATGTCCCAGTGTTCTGGCCCATCCTGGTGATGTACTTCATCATGCTTTTCTGTATC
ACCATGAAGAGGCAAATAAAGCACATGATAAAGTACCGGTACATCCCATTCACGCATGGCAAGAGGACATACAAGGGGAA
GGAAGACGGAGGCAAGACGTTTGCGAGC
ORF - retro_cfam_1164 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.49 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSEGDSVGDSVHGKPSVVYRFFTRLGQIYQSWLDKSTPYTAVRWVVTLGLSFVYMIRVYLLQGWYIVTYA |
| MSEGDSVGDSVHGKPSVVYRFFTRLGQIYQSWLDKSTPYTAVR.VVTLGLSFVYMIRVYLLQGWYIVTYA | |
| Retrocopy | MSEGDSVGDSVHGKPSVVYRFFTRLGQIYQSWLDKSTPYTAVR*VVTLGLSFVYMIRVYLLQGWYIVTYA |
| Parental | LGIYHLNLFIAFLSPKVDPSLMEDSDDGPSLPTKQNEEFRPFIRRLPEFKFWHAATKGILVAMACTFFEA |
| LGIYHLNLFIAFLSPKVDPSLMEDSDDGPSLPTKQNEEFRPFIRRLPEFKFWHAATKGILVAMACTFFEA | |
| Retrocopy | LGIYHLNLFIAFLSPKVDPSLMEDSDDGPSLPTKQNEEFRPFIRRLPEFKFWHAATKGILVAMACTFFEA |
| Parental | FNVPVFWPILVMYFIMLFCITMKRQIKHMIKYRYIPFTHGKRTYKGKEDGGKTFAS |
| FNVPVFWPILVMYFIMLFCITMKRQIKHMIKYRYIPFTHGKRTYKGKEDGGKTFAS | |
| Retrocopy | FNVPVFWPILVMYFIMLFCITMKRQIKHMIKYRYIPFTHGKRTYKGKEDGGKTFAS |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012049_cerebellum | 6 .34 RPM | 13 .90 RPM |
| SRP017611_brain | 3 .89 RPM | 11 .11 RPM |
| SRP017611_kidney | 9 .11 RPM | 21 .07 RPM |
| SRP017611_liver | 5 .87 RPM | 15 .59 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1164 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1164 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1164 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009307 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000019395 | 1 retrocopy |
retro_cfam_1164 ,
|
| Macropus eugenii | ENSMEUG00000006273 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000001472 | 1 retrocopy |