RetrogeneDB ID: | retro_cfam_2166 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:56898862..56899912(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000014077 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCT2 | ||
| Ensembl ID: | ENSCAFG00000000432 | ||
| Aliases: | None | ||
| Description: | chaperonin containing TCP1, subunit 2 (beta) [Source:HGNC Symbol;Acc:1615] |
Retrocopy-Parental alignment summary:
>retro_cfam_2166
GCCTTAGAAGCTGTTCTCAGACTGAAAGGCTCTGGTAATCTGGAGGCAATTCATGTCATCAAGAAGCTAGGAGGAAGTCT
GGCAGATTCCTATTTAGATGAAAGCTTTCTGTTGGATAAAAAATTGGAGTAAATCAACCAAAGCGAATTGAAAATGCTAA
AATTCTCATTGCGAATACTGGTATGGATACAGCCAAAATAAAGATATTTGGTTCCAGGGTAAGAGTTGATTCTACAGCAA
AGGTTGGTGAAATAGAATATGCCGAAAAGGAAAAAATGAAGAAGAAAGTTGAACGTATTCTTAAGCATGGGATAAATTGC
TTTATTAACAGGCAGTTAATTTACAATTATCCTGAACAGCTCTTTGGTGCTGCTGGTGTTATGGCTATCGAACATACAGA
TTTTGCAGGTGTGGAATGCCTAGCTCTTGTTATAGGTGGTGAAATTGCCTCTACCTTTGACCACCCAGAACTAGTGAAAC
TTGGAAGTTGCAAGCTTATTGAGGAAGTCATGATTGGAGAAGATAAACTTATCCACTTTTCTGGGGTAGCCCTTGGTGAA
GCTTGTACCATTGTTTTTGGGTGGTGCCACTCAACAGATTTTAGATGAAGCAGAAAGATCTTTGCATGATGCTCTTTGTG
TTCTTGCCCAAACTGTGAAGGATTCTAGAACAGTGTATGGAGGAGGCTGTTCTGAGATGCTGATGGCTCATGCTGTGACA
CAGCTTGCCAGTAGAACACCAGGCAAAGAAGCTGTTGCAATGGAGTCTTATGCTAAAGCACTGAGAATGTTGCCAACTAT
CATAGCTGATAACACAGGCTACAACAGTGTAGACCTGGTGGCCCAGCTGCGAGCTGCCCACAGTGAAGGTAACACAACTG
CTGTCCTGGATATGAAGGAAGGTACCATCGGAGATATGGCAGTACTGGGTATAACAGAAAGTTTCCAAGTGAAGCGACAA
GTTCTTTTGAGTGCAGCTGAAGCAGCAGAGGTGATTCTGCGTGTGGACAACGCAGCACCAAGGAAACGTGTTCCTGATCA
CCACCCCTGT
ORF - retro_cfam_2166 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.65 % |
| Parental protein coverage: | 65.98 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AVEAVLRLKGSGNLEAIHVIKKLGGSLADSYLDEGFLLDKK-IGVNQPKRIENAKILIANTGMDTDKIKI |
| A.EAVLRLKGSGNLEAIHVIKKLGGSLADSYLDE.FLLDKK.IGVNQPKRIENAKILIANTGMDT.KIKI | |
| Retrocopy | ALEAVLRLKGSGNLEAIHVIKKLGGSLADSYLDESFLLDKK<IGVNQPKRIENAKILIANTGMDTAKIKI |
| Parental | FGSRVRVDSTAKVAEIEHAEKEKMKEKVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHADFAGVE |
| FGSRVRVDSTAKV.EIE.AEKEKMK.KVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEH.DFAGVE | |
| Retrocopy | FGSRVRVDSTAKVGEIEYAEKEKMKKKVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHTDFAGVE |
| Parental | RLALVTGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIV-LRGATQQILDEAERSL |
| .LALV.GGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIV.L.GATQQILDEAERSL | |
| Retrocopy | CLALVIGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIV>LGGATQQILDEAERSL |
| Parental | HDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAVAMESYAKALRMLPTIIADNAGYDSAD |
| HDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAVAMESYAKALRMLPTIIADN.GY.S.D | |
| Retrocopy | HDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAVAMESYAKALRMLPTIIADNTGYNSVD |
| Parental | LVAQLRAAHSEGNTTAGLDMKEGTIGDMAVLGITESFQVKRQVLLSAAEAAEVILRVDNIIKAAPRKRVP |
| LVAQLRAAHSEGNTTA.LDMKEGTIGDMAVLGITESFQVKRQVLLSAAEAAEVILRVDN...AAPRKRVP | |
| Retrocopy | LVAQLRAAHSEGNTTAVLDMKEGTIGDMAVLGITESFQVKRQVLLSAAEAAEVILRVDN---AAPRKRVP |
| Parental | DHHPC |
| DHHPC | |
| Retrocopy | DHHPC |
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 .00 RPM | 93 .70 RPM |
| SRP017611_brain | 0 .16 RPM | 74 .95 RPM |
| SRP017611_kidney | 0 .07 RPM | 207 .22 RPM |
| SRP017611_liver | 0 .07 RPM | 62 .36 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2166 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2166 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2166 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000000432 | 2 retrocopies |
retro_cfam_1969, retro_cfam_2166 ,
|
| Choloepus hoffmanni | ENSCHOG00000006098 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000001715 | 2 retrocopies | |
| Loxodonta africana | ENSLAFG00000006688 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000008364 | 1 retrocopy |