RetrogeneDB ID: retro_cjac_560

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81373868..81374642(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004593
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARRDC3
• Ensembl ID: ENSCJAG00000010525
• Aliases: None
• Description: None

Sequence

>retro_cjac_560
GTGATGGGAAAGGTGAAAAGTTTGACAATAAGTTTTGACTGTGTTAATGACAGTAATGTCCCTGTGTATTCTAGTGAAGA
TATCATCTCAAGAAGGGTAAATTTAGAAGTTACTGGCAAAATCAGAGTAAAATCTCTTAAAATTCATGCAAGAGGATGTT
TAGAAGTATGCTTGGCTGAATCTAGAAACACTGGCACCAATACTGCCTGTACACAGAATTACATTGCAGAAGTAGAATAT
TTCAACCATAAAGATATCTTAATTGGGCATGAAAGAGACAATAATAATTCCAAAGAAGGCTTCAAGGCTATTCATTCAGG
AAGGCATGCATATGCATTCAGCCGTAAGCGTCCACAGATACCACTTGCTACTTCATTTAAAGGCAGCCATGGTGTGTGCA
CTGTTGTGTGAAAGCTGAATCTCACAGGCCTTGGCTACTAACAGTAACATCAAAGAAAAAATTTACAGTCTTTGAATATA
TAAATATGAACACTCCTTCATCACTGTCACCCAAGCAGGCACAGAAGAAAAGACACTAGGTTGCTGGTTTTCTACCTCAG
GCTCAATATCCTTAAGTGCCAAAATTGAAAGGAAGGGCTATTACATGGGTGAATCAACTCAGATATTTGCTAAGACTGAG
AACTGCTCTTCCCAAATGCTGGTGCCAGAGTCAGACATTACCAAACACACTTTCGTGCCAAAGGGGAAATGAAGGAAGTA
AAACAGTGCATGGCTAACTTGCATGAGGAATCCTTGTCATTTGGAAAGAGAGAT

Alignment

ORF - retro_cjac_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73. %
• Parental protein coverage: 62.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLGKVKSLTISFDCLNDSNVPVYSSGDTVSGRVNLEVTGEIRVKSLKIHARGHAKVRWTESRNAGSNTAY
          V.GKVKSLTISFDC.NDSNVPVYSS.D..S.RVNLEVTG.IRVKSLKIHARG...V...ESRN.G.NTA.
Retrocopy VMGKVKSLTISFDCVNDSNVPVYSSEDIISRRVNLEVTGKIRVKSLKIHARGCLEVCLAESRNTGTNTAC

Parental  TQNYTEEVEYFNHKDILIGHERDDDNSEEGFHTIHSGRHEYAFSFELPQTPLATSFEGRHG-SVRYWVKA
          TQNY..EVEYFNHKDILIGHERD..NS.EGF..IHSGRH.YAFS...PQ.PLATSF.G.HG..V...VKA
Retrocopy TQNYIAEVEYFNHKDILIGHERDNNNSKEGFKAIHSGRHAYAFSRKRPQIPLATSFKGSHG<CVHCCVKA

Parental  ELHRPWLLPVKLKKEFTVFEHIDINTPSLLSP-QAGTKEKTLCCWFCTSGPISLSAKIERKGYTPGESIQ
          E.HRPWLL.V..KK.FTVFE.I..NTPS.LSP.QAGT.EKTL.CWF.TSG.ISLSAKIERKGY..GES.Q
Retrocopy ESHRPWLLTVTSKKKFTVFEYINMNTPSSLSP<QAGTEEKTLGCWFSTSGSISLSAKIERKGYYMGESTQ

Parental  IFAEIENCSSRMVVPKAAI-YQTQAFYAKGKMKEVKQLVANLRGESLSSGKTE
          IFA..ENCSS.M.VP...I.YQT..F.AKG.MKEVKQ..ANL..ESLS.GK..
Retrocopy IFAKTENCSSQMLVPESDI<YQTH-FRAKGEMKEVKQCMANLHEESLSFGKRD

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	96.52 RPM
SRP051959_heart	0.00 RPM	36.45 RPM
SRP051959_kidney	0.00 RPM	282.74 RPM
SRP051959_liver	0.00 RPM	58.53 RPM
SRP051959_lung	0.00 RPM	240.34 RPM
SRP051959_lymph_node	0.00 RPM	91.69 RPM
SRP051959_skeletal_muscle	0.00 RPM	80.91 RPM
SRP051959_spleen	0.00 RPM	164.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_560 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010525	1 retrocopy	retro_cjac_560 ,
Callithrix jacchus	ENSCJAG00000036002	1 retrocopy	retro_cjac_1762,
Nomascus leucogenys	ENSNLEG00000013887	1 retrocopy	retro_nleu_2985,
Pongo abelii	ENSPPYG00000015628	1 retrocopy	retro_pabe_3452,