RetrogeneDB ID: retro_cjac_2579

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:149446578..149448063(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018200
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2579
ATGGCGTCCCTTTCCCTTACACCTGTTAACATCTTCAAGGCAGGAGCTGATGAAGAGAGAGCAGAGACAGCTCGTCTGTC
TTCTTTTATTGGTGCCATCGCTGTTGGAGACTTGGTAAAAAGCACCTTGGGACCCAAAGGCATGGACAAAATTCTTCTAA
GCAGTGGACGAGATGCCTCTCTTATGGTAACAAATGATGGTGCCACTATTCTAAAAAACATTGGTGTTGACAATCCAGCA
GCTAAAGTTTTAGTTGATATGTCAAGGGTTCAAGATGATGATGTTGGTGATGGCACTACCTCTGTTACTGTTTTAGCAGC
AGAATTATTAAGGGAAGCAGAATCTTTAATTGCAAAAAAGATTCATCCACAGACCATCATAGCAGGTTGGAGAGAAGCCA
CAACGGCTGCAAAAGAGGCTCTGTTGAGTTCTGCAGTCGATCATGGTTCCAACGAAGTTAAATTCCGTCAAGATTTAATG
AATATTGTGGGCACAACATTATCCTCAAAAATTCTTACTCATCACAAAGACCACGTTACTCAATTAGCTGTAGAAGCGGT
TCTCAGACTGAAAGGCTCTGGCAACCTGGAGGCAATTCATATTATCAAGAAGCTAGGAGGAAGTCTGGCAGATTCCTATT
TAGATGAAGACTTTCTATTGGATAAAAACATTAGAGTAAATCAACCAAAACGAATTGAAAATGCTAAAATTCTTTTTGCA
AATACTGGTATGGATACAGACAAAATAAAGATATTTGGTTCCCGGGTAAGAGTTGATTCTACAGCAAAGGTTGCAGAAAT
AGAACATGCGGAAAAGGAAAAAATGAAGGAGAAAGTTGAACGTATTCTTAAGCATGGAATAAATTGCTTCAGTAACAGGC
AGTTAATATATAATTACCCTGAACAGCTCTTCTGTGCTGCTGGTGTCATGGCTATTGAGCACGCAGATTTTGCAGGCGTG
GAATGCCTAGCTCTTGTCACAGGTGGTGAAATTGCCTCTACCTTTGATCATCCAGAACTGGTAAAGCTTGGAAGTTGCAA
ATTTATTGAGGAAGTCATGATTGGAGAAAACAAACTCATTCACTTTTCTGGGGTTGCCCTTGGTGAGGCTTGTACCATTG
TTGTGCGTGATGCCACTCAACAAATTTTAGATGAAGCTGAAAGATCTTTGCATGATGCTCTTTCTGTTCTTACACAAACC
GTAAAGGATTCTAGAACAGTTTATGGAGGAGGCTGTTGGGAGATGTTGATGGCTCATGCTGTGACACAGCTTGCCAATAG
AACACCAGGCGAAGAAGCTGTTGCAATGGAGGCTTATGCTAAAGCACTGAGAATGTTGCCAACCATCATAGCTGACAATG
CAGGCTATGACAGTGCAGACCTAGTGGCACAGCTCAGAGCTACTCACAGTGAAGGCAATACCACTGCTGGACTAGACATG
AGGGAAGGCACCATTGGAGATATGGCTCTCCTAGGTATAACAGAG

Alignment

ORF - retro_cjac_2579 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.56 %
• Parental protein coverage: 92.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLSLTPVNIFKAGADEERAETARLSSFIGAIAIGDLVKSTLGPKGMDKILLSSGRDASLMVTNDGATI
          MASLSLTPVNIFKAGADEERAETARLSSFIGAIA.GDLVKSTLGPKGMDKILLSSGRDASLMVTNDGATI
Retrocopy MASLSLTPVNIFKAGADEERAETARLSSFIGAIAVGDLVKSTLGPKGMDKILLSSGRDASLMVTNDGATI

Parental  LKNIGVDNPAAKVLVDMSRVQDDEVGDGTTSVTVLAAELLREAESLIAKKIHPQTIIAGWREATKAAREA
          LKNIGVDNPAAKVLVDMSRVQDD.VGDGTTSVTVLAAELLREAESLIAKKIHPQTIIAGWREAT.AA.EA
Retrocopy LKNIGVDNPAAKVLVDMSRVQDDDVGDGTTSVTVLAAELLREAESLIAKKIHPQTIIAGWREATTAAKEA

Parental  LLSSAVDHGSDEVKFRQDLMNIAGTTLSSKLLTHHKDHFTKLAVEAVLRLKGSGNLEAIHIIKKLGGSLA
          LLSSAVDHGS.EVKFRQDLMNI.GTTLSSK.LTHHKDH.T.LAVEAVLRLKGSGNLEAIHIIKKLGGSLA
Retrocopy LLSSAVDHGSNEVKFRQDLMNIVGTTLSSKILTHHKDHVTQLAVEAVLRLKGSGNLEAIHIIKKLGGSLA

Parental  DSYLDEGFLLDKKIGVNQPKRIENAKILIANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVE
          DSYLDE.FLLDK.I.VNQPKRIENAKIL.ANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVE
Retrocopy DSYLDEDFLLDKNIRVNQPKRIENAKILFANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVE

Parental  RILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHADFAGVERLALVTGGEIASTFDHPELVKLGSCKLIE
          RILKHGINCF.NRQLIYNYPEQLF.AAGVMAIEHADFAGVE.LALVTGGEIASTFDHPELVKLGSCK.IE
Retrocopy RILKHGINCFSNRQLIYNYPEQLFCAAGVMAIEHADFAGVECLALVTGGEIASTFDHPELVKLGSCKFIE

Parental  EVMIGEDKLIHFSGVALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHA
          EVMIGE.KLIHFSGVALGEACTIV.R.ATQQILDEAERSLHDAL.VL.QTVKDSRTVYGGGC.EMLMAHA
Retrocopy EVMIGENKLIHFSGVALGEACTIVVRDATQQILDEAERSLHDALSVLTQTVKDSRTVYGGGCWEMLMAHA

Parental  VTQLANRTPGKEAVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGNTTAGLADMREGTIGDMA
          VTQLANRTPG.EAVAME.YAKALRMLPTIIADNAGYDSADLVAQLRA.HSEGNTTAGL.DMREGTIGDMA
Retrocopy VTQLANRTPGEEAVAMEAYAKALRMLPTIIADNAGYDSADLVAQLRATHSEGNTTAGL-DMREGTIGDMA

Parental  LLGITE
          LLGITE
Retrocopy LLGITE

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	0.00 RPM	28.20 RPM
SRP051959_heart	0.00 RPM	34.43 RPM
SRP051959_kidney	0.11 RPM	34.88 RPM
SRP051959_liver	0.04 RPM	36.15 RPM
SRP051959_lung	0.05 RPM	29.59 RPM
SRP051959_lymph_node	0.07 RPM	29.13 RPM
SRP051959_skeletal_muscle	0.11 RPM	28.78 RPM
SRP051959_spleen	0.04 RPM	31.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2579 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2579 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,