RetrogeneDB ID: retro_cjac_1854

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:148263485..148264492(+)
• Located in intron of: ENSCJAG00000015215

Retrocopy information

• Ensembl ID: ENSCJAG00000015276
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCT2
• Ensembl ID: ENSCJAG00000001715
• Aliases: None
• Description: None

Sequence

>retro_cjac_1854
ATTATTAAGAAGCTAGGAGGAAGTTTGGCAGATTGTTTAGATGAAGACTTTCTGTTGGATAAAAAAATTGGAGTGAATCA
ACCAAAATGAGTTGAAAAATGCTAAAATTCTTATTGCAGACAATTTTTTCTGTATGGATACAGACAAAATAAAGATATTT
GGTTCCTAGGAAGAGTTGGTTCTACAGCAAAGATTACAGAAATAGAACATGTGGAAAAGGAAAAAATGAAGGAGAAAGTT
GAATGTATTCTTAAGCATGGAATAAATTGCTTTATTAACAGGCAGTTAATTTATAATTATCTTGAACAGCTCTTTGGCGC
TGCTGGTGTCATGGCTATTGAGCATGCAGATTTTGCACGTGTGGAACACCTAGTTCTTGTCATGGGTGGTGAAATTGCCT
CTACCTTTGATCACCCAGAACTGGTGAAGCTTGGAAGCTGCAAACTTATCAAGGAAGTCATGATTGGAGAAGACAAACTT
ATTCACTTTTCTGGGGTTGCCCTTGGTGAGGCTTATACCATTGTTTTCATGGTGCCACTCAACAAATTTTAGATGAAGCA
GAAAGATCTTTGCATGATGCTGTTTGTGTTCTTGCACAAACTGTAAAGGACTCTAGAACAGTTTATGGAGTAGGCTTTTC
AGAGATGTTGATGGCTCATGCTGTGACACAGCTTGCTAATAGAACACCAGGCAAAGAAGCTGTTGCAGTGGAGTCTTATG
CTAAAGCACTGAGAATGTTGCCAAACATCATAGCTGACAATGCAGGCTATGACAGTGCAGACCTAGTGGCACAGCTCAGA
GCTGCTCACCATGAAGGCAACACCACTGCTGGACTGGATAGGAGGGAAGGCCCCATTGGAGATATGGCTCTCCTGGGTAT
AACAGAAAGTTTTCAAGTAAAGCAACAAGTTCTTCTAAGTGCAGCTGAAGCAGCAGAGGTGATTCTACATGTGGACAACA
TCATCAAAGTGGCACCCAGGAAGCTTGTCCCTGATCACCACCTGTGT

Alignment

ORF - retro_cjac_1854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 68.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IIKKLGGSLADSYLDEGFLLDKKIGVNQPKRIE-NAKILIANTG--MDTDKIKIFGS-RVRVDSTAKVAE
          IIKKLGGSLAD..LDE.FLLDKKIGVNQPK..E.NAKILIA.....MDTDKIKIFGS...RV.STAK..E
Retrocopy IIKKLGGSLADC-LDEDFLLDKKIGVNQPK*VE>NAKILIADNFFCMDTDKIKIFGS<LGRVGSTAKITE

Parental  IEHAEKEKMKEKVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHADFAGVERLALVTGGEIASTFD
          IEH.EKEKMKEKVE.ILKHGINCFINRQLIYNY.EQLFGAAGVMAIEHADFA.VE.L.LV.GGEIASTFD
Retrocopy IEHVEKEKMKEKVECILKHGINCFINRQLIYNYLEQLFGAAGVMAIEHADFARVEHLVLVMGGEIASTFD

Parental  HPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIVL-RGATQQILDEAERSLHDALCVLAQTVKDSR
          HPELVKLGSCKLI.EVMIGEDKLIHFSGVALGEA.TIV...GATQQILDEAERSLHDA.CVLAQTVKDSR
Retrocopy HPELVKLGSCKLIKEVMIGEDKLIHFSGVALGEAYTIVF<HGATQQILDEAERSLHDAVCVLAQTVKDSR

Parental  TVYGGGCSEMLMAHAVTQLANRTPGKEAVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGNTT
          TVYG.G.SEMLMAHAVTQLANRTPGKEAVA.ESYAKALRMLP.IIADNAGYDSADLVAQLRAAH.EGNTT
Retrocopy TVYGVGFSEMLMAHAVTQLANRTPGKEAVAVESYAKALRMLPNIIADNAGYDSADLVAQLRAAHHEGNTT

Parental  AGLDMREGTIGDMALLGITESFQVKRQVLLSAAEAAEVILRVDNIIKAAPRKRVPDHHPC
          AGLD.REG.IGDMALLGITESFQVK.QVLLSAAEAAEVIL.VDNIIK.APRK.VPDHH.C
Retrocopy AGLDRREGPIGDMALLGITESFQVKQQVLLSAAEAAEVILHVDNIIKVAPRKLVPDHHLC

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
SRP051959_colon	2.48 RPM	28.20 RPM
SRP051959_heart	1.82 RPM	34.43 RPM
SRP051959_kidney	5.79 RPM	34.88 RPM
SRP051959_liver	0.54 RPM	36.15 RPM
SRP051959_lung	2.33 RPM	29.59 RPM
SRP051959_lymph_node	0.02 RPM	29.13 RPM
SRP051959_skeletal_muscle	4.11 RPM	28.78 RPM
SRP051959_spleen	0.63 RPM	31.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1854 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1854 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,