RetrogeneDB ID: | retro_cfam_1442 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 31:3991102..3992288(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HMGCS2 | ||
| Ensembl ID: | ENSCAFG00000010096 | ||
| Aliases: | None | ||
| Description: | 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) [Source:HGNC Symbol;Acc:5008] |
Retrocopy-Parental alignment summary:
>retro_cfam_1442
AGAATCTTATGGAGAGATAGCATTTTGTATGATTGCATTGGGCATTTAGAAGTTGGAACAGAGACAATCATCGACAAATC
AAAATCCGTGAAGACTAATTTGATGCAGCTCTTTGAGGAGTCTGGGAACACAGATATAGAAGGAATAGATACAACTAATG
CATGCTATGGAAGCACAGCTGCTGTCTTCAATGGGGTTAATTGGATTGAGTCCAGCTCCTGGGATGGACAGTATGCCCTG
GTAGTTGCGGGAGATATTGCTGTATATGCCACAGGAAATTCTAGACCTACAGGTGAAGTGAGATCTGCTGCTCTGCTAAT
TGGGGCAAATGCGCCTTTAATTTTTGACCAAGGACTTCGTGGGACACATATGTAACATGCCTATGACTTTTACAAGCCTG
ACATGCTTTCGGAATATCCTATAGTAGATGGGAAACTCTCCATACAGTGGTACTTCGGTGCACTAGACCGCTACTATTCT
GTCTATCACAAAAAGATCCGAGCCCAGTGGCAGAAACAGGGAAATGATAAAGACTTTACCTTGAATGATTTTGGTTTCAT
GATCTTCCACTCACCCTACTGTAAGCTGGTTCAGAAGTCTCTAGCTCAGATTTTGCTGAATGACATCCTTAATGACCAGA
ACAGAGATAAAAATAGTATCTATAATGGCCTGGAAGCCTTTGGGGATGTTAAATTAGAAGATACTTAGTTTGATAGCGAT
GTGGAAAAGGCATTTACGAAGGCTAGTGCTGAACTCTAATCAGAAAACAAAGGCATCTTTGCTTGTGTCAAATCAAAATG
GAAATATGTACACATCGTCTGTTTATGGCTCCCTCGCTTCTGTTCTAGCACAGTACTCACCTCAACAGCTGGCAGGAAAG
AGGATTGGTGTGTTCTCTTATGGTTCTGGTTTGGCTGCCACCCTGTACTCCCTTGGAGTTATGCAAGATGCCACACCAGG
GTCTGGTCTTGATAAAATAACAGCAAGTTTATGTGACCTCAAATCAAGACTTGACTCAAGAACTTATGTGGAACCAGATG
TCTTTGCTGAAAACATGAAGCTCAGAGAGCACACTCATCACTTGATGAACTATATTCCTCAGAGCTCAGCAGATTCCCTC
TTCGAAGGGACCTGGTACCTCGTCAGAGTGGATGAGAAGCACAGGAGGACCTATGCCCAGAGCCCT
ORF - retro_cfam_1442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.19 % |
| Parental protein coverage: | 77.95 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RLMERTQLPWDSVGWLEVGTETIIDRSKAVKTVLMELFQDSGNTDIEGIDTTNACYGGTASLFNAANWVE |
| R...R.....D..G.LEVGTETIID.SK.VKT.LM.LF..SGNTDIEGIDTTNACYG.TA..FN..NW.E | |
| Retrocopy | RILWRDSILYDCIGHLEVGTETIIDKSKSVKTNLMQLFEESGNTDIEGIDTTNACYGSTAAVFNGVNWIE |
| Parental | SSSWDGRYAMVVCGDIAVYPSGNARPTGGAGAVAMLVGPKAPLTLERGLRGTHMENVYDFYKPDAATEYP |
| SSSWDG.YA.VV.GDIAVY..GN.RPTG.....A.L.G..APL....GLRGTHM...YDFYKPD...EYP | |
| Retrocopy | SSSWDGQYALVVAGDIAVYATGNSRPTGEVRSAALLIGANAPLIFDQGLRGTHM*HAYDFYKPDMLSEYP |
| Parental | IVDGKLSIQCYLRALDRCYTLYRQKIQKQWKQAGIDRPFTLDDLQFMIFHTPFCKIVQKSLARLMFNDFL |
| IVDGKLSIQ.Y..ALDR.Y..Y..KI..QW...G.D..FTL.D..FMIFH.P.CK.VQKSLA....ND.L | |
| Retrocopy | IVDGKLSIQWYFGALDRYYSVYHKKIRAQWQKQGNDKDFTLNDFGFMIFHSPYCKLVQKSLAQILLNDIL |
| Parental | SASSDTQTSLYKELETFRGLKLEDTYTNKDMDKALQKVS-LDSFNKKTKASLYLSTHNGNMYTSSLYGCL |
| ........S.Y..LE.F...KLEDT....D..KA..K.S.L.S.N.KTKASL..S..NGNMYTSS.YG.L | |
| Retrocopy | NDQNRDKNSIYNGLEAFGDVKLEDT*FDSDVEKAFTKAS>LNS-NQKTKASLLVSNQNGNMYTSSVYGSL |
| Parental | ASLLSQHSAQDLAGSRIGAFSYGSGLAASFFSFRVSQDASPGSPLEKLVSSMSDLPKRLASRKRMSPQEF |
| AS.L.Q.S.Q.LAG.RIG.FSYGSGLAA...S..V.QDA.PGS.L.K...S..DL..RL.SR....P..F | |
| Retrocopy | ASVLAQYSPQQLAGKRIGVFSYGSGLAATLYSLGVMQDATPGSGLDKITASLCDLKSRLDSRTYVEPDVF |
| Parental | TEIMDQREQFYHKVNFSPPGDTSSLFPGTWYLERVDELYRRKYARRP |
| .E.M..RE...H..N..P.....SLF.GTWYL.RVDE..RR.YA..P | |
| Retrocopy | AENMKLREHTHHLMNYIPQSSADSLFEGTWYLVRVDEKHRRTYAQSP |
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 | 0 .08 RPM | 0 .08 RPM |
| SRP017611_brain | 0 .16 RPM | 0 .08 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .80 RPM |
| SRP017611_liver | 0 .22 RPM | 1566 .43 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1442 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1442 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1442 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000010096 | 1 retrocopy |
retro_cfam_1442 ,
|
| Echinops telfairi | ENSETEG00000005380 | 1 retrocopy |