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 symbol: CCT2
• Ensembl ID: ENSCAFG00000000432
• Aliases: None
• Description: chaperonin containing TCP1, subunit 2 (beta) [Source:HGNC Symbol;Acc:1615]

Sequence

>retro_cfam_2166
GCCTTAGAAGCTGTTCTCAGACTGAAAGGCTCTGGTAATCTGGAGGCAATTCATGTCATCAAGAAGCTAGGAGGAAGTCT
GGCAGATTCCTATTTAGATGAAAGCTTTCTGTTGGATAAAAAATTGGAGTAAATCAACCAAAGCGAATTGAAAATGCTAA
AATTCTCATTGCGAATACTGGTATGGATACAGCCAAAATAAAGATATTTGGTTCCAGGGTAAGAGTTGATTCTACAGCAA
AGGTTGGTGAAATAGAATATGCCGAAAAGGAAAAAATGAAGAAGAAAGTTGAACGTATTCTTAAGCATGGGATAAATTGC
TTTATTAACAGGCAGTTAATTTACAATTATCCTGAACAGCTCTTTGGTGCTGCTGGTGTTATGGCTATCGAACATACAGA
TTTTGCAGGTGTGGAATGCCTAGCTCTTGTTATAGGTGGTGAAATTGCCTCTACCTTTGACCACCCAGAACTAGTGAAAC
TTGGAAGTTGCAAGCTTATTGAGGAAGTCATGATTGGAGAAGATAAACTTATCCACTTTTCTGGGGTAGCCCTTGGTGAA
GCTTGTACCATTGTTTTTGGGTGGTGCCACTCAACAGATTTTAGATGAAGCAGAAAGATCTTTGCATGATGCTCTTTGTG
TTCTTGCCCAAACTGTGAAGGATTCTAGAACAGTGTATGGAGGAGGCTGTTCTGAGATGCTGATGGCTCATGCTGTGACA
CAGCTTGCCAGTAGAACACCAGGCAAAGAAGCTGTTGCAATGGAGTCTTATGCTAAAGCACTGAGAATGTTGCCAACTAT
CATAGCTGATAACACAGGCTACAACAGTGTAGACCTGGTGGCCCAGCTGCGAGCTGCCCACAGTGAAGGTAACACAACTG
CTGTCCTGGATATGAAGGAAGGTACCATCGGAGATATGGCAGTACTGGGTATAACAGAAAGTTTCCAAGTGAAGCGACAA
GTTCTTTTGAGTGCAGCTGAAGCAGCAGAGGTGATTCTGCGTGTGGACAACGCAGCACCAAGGAAACGTGTTCCTGATCA
CCACCCCTGT

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2166 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2166 has 0 orthologous retrocopies within eutheria group .

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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	retro_chof_272,
Callithrix jacchus	ENSCJAG00000001715	2 retrocopies	retro_cjac_1854, retro_cjac_2579,
Loxodonta africana	ENSLAFG00000006688	1 retrocopy	retro_lafr_351,
Myotis lucifugus	ENSMLUG00000008364	1 retrocopy	retro_mluc_2248,