RetrogeneDB ID: retro_cjac_2253

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:88374217..88375325(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KIAA0020
• Ensembl ID: ENSCJAG00000010917
• Aliases: None
• Description: KIAA0020 [Source:HGNC Symbol;Acc:29676]

Sequence

>retro_cjac_2253
TATGGGAACACATTTCGGCTTTACAAGTCAGCAGATCACTCAACTCTGGACAAAGTATTAGAGGTACAGCCAGAGAAACT
ACAGCTTATTATGGATGAAATGAAACAGATTCTAACTCCAGTGGCCCAAAAGGGAGCTGTGATTAAGCACTCTTTGGTGC
ATAAAGTATTCTTGGACTTTTTTATCTATGTACCCCCCAAACTCAGAAACTATTGAGGCCATCTGTGAAGTGGTGGTAAA
CCTGGCACACACAAACGATGGCGCCAGAGTGGCAATGAAGTGCCTGTGGCATGGTACCCCCAAGGACAGGAAAGTGATTG
TGAAAACAATGAAGACAACGTTGAAAAGGTGGCTAATGGCCAATACTCCCATTTGGTTTTACTGGTGGTATTTGATTGTA
CTGCAACTAAGCTTGTGAAGCAGATAATCATATCAGAAATTATCAGTTTGTTGCCTAACACAGTAAATGATAAATATGGA
AGGAAGGTCCTATTATACTTACTAAGCCCCAGAGATCCTGCGCATACAGTTTGAGAAATCATTGAAGTTGTGCAAAAAGG
AGATGGAAATGCACACAGTAAGAAAGATATAAGAGGTCTGCAGACGGGAGCTCCTAGAATCCATTTCTCCAGCGTTGTTA
AGCTACCTGCAAGAACACACCCAAGAGGTGGTGCTACATAAGTGTGCGTGTGTGTCTGACATTCTGGGATCTGCCACTGG
AGATGTTCGGCCTGCCATGAATGCCATCGCGAGCTTGGCAGCAGCAGAACTGCACCCCGCTGGCAAGGACAGAGAGCTTC
ACATGGCAGAACATCCTGCAGGACATCTAGTTCTGAAGTGGTTAACAGAGCAAGATAAAAAGATGAAAGAAAATGGGAGA
GAAGGTGGTTTTGCAAAAACACGTGTAGAAGAGCATGTTGGTATGAAGACCTAAAGTCTTGGGCTAGTGTAAATCAAGGT
GCCATTATTCTTTCCAGCCTCCCTCCAGAGTTATGACCCAGAAGTTGCAAACAAAGTCAAAGCTGCACTGAAAAGCTTGA
TTCCTACATTGGAAAAAATCAAAAGCACCAGCAAAGGAATAGAAACTCTACTTGAAAAACTGAGCACA

Alignment

ORF - retro_cjac_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.43 %
• Parental protein coverage: 57.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YGNTFQLYKSADHPTLDKVLEVRPEKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYA-PPKLR
          YGNTF.LYKSADH.TLDKVLEV.PEKL.LIMDEMKQILTP.AQK.AVIKHSLVHKVFLDFF.Y..PP...
Retrocopy YGNTFRLYKSADHSTLDKVLEVQPEKLQLIMDEMKQILTPVAQKGAVIKHSLVHKVFLDFFIYV>PPN--

Parental  SEMIEAIREAVVYLAHTHDGARVAMHCLWHGTPKDRKVIVKTMKTY-IEKVANGQYSHLVLLAAFDCIDD
          SE.IEAI.E.VV.LAHT.DGARVAM.CLWHGTPKDRKVIVKTMKT...EKVANGQYSHLVLL..FDC...
Retrocopy SETIEAICEVVVNLAHTNDGARVAMKCLWHGTPKDRKVIVKTMKTT<VEKVANGQYSHLVLLVVFDCTA-

Parental  TKLVKQIIVSEIISSLPSIVNDKYGRKVLLYLLSPRDPAHTVREIIEVLQKGDGNAHSKKDT-EVRRREL
          TKLVKQII.SEIIS.LP..VNDKYGRKVLLYLLSPRDPAHTV.EIIEV.QKGDGNAHSKKD..EV.RREL
Retrocopy TKLVKQIIISEIISLLPNTVNDKYGRKVLLYLLSPRDPAHTV*EIIEVVQKGDGNAHSKKDI>EVCRREL

Parental  LESISPALLSYLQEHTQEVVLDKSACVLVSDILGSATGDVQPAMNAIASLAATELHPGGKDGELHIAEHP
          LESISPALLSYLQEHTQEVVL.K.ACV..SDILGSATGDV.PAMNAIASLAA.ELHP.GKD.ELH.AEHP
Retrocopy LESISPALLSYLQEHTQEVVLHKCACV--SDILGSATGDVRPAMNAIASLAAAELHPAGKDRELHMAEHP

Parental  AGHLVLKWLIEQDKKMKENGREGCFAKTLV-EHVGMKS-LKSWASINRGAIILSSL-LQSCDPEVANKVK
          AGHLVLKWL.EQDKKMKENGREG.FAKT.V.EHVGMK..LKSWAS.N.GAIILSSL.LQS.DPEVANKVK
Retrocopy AGHLVLKWLTEQDKKMKENGREGGFAKTRVEEHVGMKT<LKSWASVNQGAIILSSL>LQSYDPEVANKVK

Parental  AALKSLIPALEKTKSTSKGVEALLEKLTT
          AALKSLIP.LEK.KSTSKG.E.LLEKL.T
Retrocopy AALKSLIPTLEKIKSTSKGIETLLEKLST

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	0.71 RPM	10.41 RPM
SRP051959_heart	0.67 RPM	10.09 RPM
SRP051959_kidney	1.04 RPM	14.78 RPM
SRP051959_liver	0.71 RPM	10.83 RPM
SRP051959_lung	1.02 RPM	11.21 RPM
SRP051959_lymph_node	0.46 RPM	11.44 RPM
SRP051959_skeletal_muscle	0.46 RPM	10.42 RPM
SRP051959_spleen	1.01 RPM	10.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2253 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012187	1 retrocopy	retro_amel_1752,
Callithrix jacchus	ENSCJAG00000010917	1 retrocopy	retro_cjac_2253 ,
Cavia porcellus	ENSCPOG00000008552	1 retrocopy	retro_cpor_1158,
Loxodonta africana	ENSLAFG00000017341	1 retrocopy	retro_lafr_1029,
Mus musculus	ENSMUSG00000041360	1 retrocopy	retro_mmus_3640,
Oryctolagus cuniculus	ENSOCUG00000004189	1 retrocopy	retro_ocun_213,
Sorex araneus	ENSSARG00000000579	1 retrocopy	retro_sara_499,