RetrogeneDB ID: retro_cjac_3083

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:74612303..74613383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSCJAG00000016181
• Aliases: None
• Description: None

Sequence

>retro_cjac_3083
TTTGCAAAACCATTTCTTGGTTGGCTGGATGGTCACTGAGATGGAATCAGTTTCTTGGCAAAGCATCTGAAGAGCCTGGC
TACTGTCCTTTCTGGGGCATGTGATGGAGAGGTTAGAATTTGGAACCTGACTAAACTGAAATGTATTCATACAATATAAG
CACATGAAGGCTTTGTATGAGGACTATGTACTCGCTGTTGTGGGGCTTCTTTTTTCACTGTTGATGGTGACAAAACTGTG
AAGTCGTGAAACATGGATGGGCCAGCCTATGGAGAGGAGGAAGAGCCATTACATACAATATTCAGAAAGACAGTATATAC
TGGGATTGATCATCACTGGAAAGAAGCTGTTTTTGCCACATGTGGACAGCAAGGAGATGTTTGGGATGAACAAATAACTA
ATCCTATATGTTCAATGACCTGGAGATTTGACAGTATAAGTAGTATTAAATTCAACCCAATTGAGACATTTCTCTTGGAA
AGTTGTGCGTCTGACAGGAATATAGTACTTTATGCTATGAGGCAAGGTACTCCTCTGAAAAAGGTTGCCTTAGATATGAG
AACAAATACAATCTGTTGGAACCCTATGGAAGCTTTCATTTTCACGGTGGCAAATGAAGACAATAACTTATTAACTTTTG
ATATGCGGGCACTGGACACTTCTGTAATGGTCCATATGAATCATGTATCTTCAGTGCTTGATGTGGATTACTCTCCCACT
GGGAAAGAGTTCATGTCTGCTAGTTTCGATAAATCTATTTGAATCTTTACTGTAGACAAAAGTCAAAGCAGGGTGGCATA
TCACACAAAGAGAATGCAACATGTTGTCTGTGTAAAACGGACTTCTGACAGCAAGTATATTATGTATGGATCTGATGAAA
TGAACATTCACCTATGTAAAGCTAATGCTTCTGAAGAATTGGGTGTGCTTACATCATGAGAAAAAGCAGCCAAGTATTAT
AGCCAGAAACTGAAGGAGAAATGTCAGCATCATCCTCATATAAAACAGATAGCTCGCCATCAACATCTACCAAAATCTAT
CTACAGCCCGATTCAGGAACAGTGCATCATGAAAGAAGCA

Alignment

ORF - retro_cjac_3083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 80.9 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAKPFLASLDGHRDGVNCLAKHPKNLATVLSGACDGEVRIWNLTQRKCIRTIQAHEGFVRGICTRFCGTS
          FAKPFL..LDGH.DG...LAKH.K.LATVLSGACDGEVRIWNLT..KCI.TI.AHEGFV.G.CTR.CG.S
Retrocopy FAKPFLGWLDGH*DGISFLAKHLKSLATVLSGACDGEVRIWNLTKLKCIHTI*AHEGFV*GLCTRCCGAS

Parental  FFTVGDDKTVKQWKMDGPGYGEEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPICSMT
          FFTV..DKTVK...MDGP.YGEEEEPLHTI..KTVYTGIDHHWKEAVFATCGQQ.D.WDEQ.TNPICSMT
Retrocopy FFTVDGDKTVKS*NMDGPAYGEEEEPLHTIFRKTVYTGIDHHWKEAVFATCGQQGDVWDEQITNPICSMT

Parental  WGFDSISSVKFNPIETFLLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNL
          W.FDSISS.KFNPIETFLL.SCASDRNIVLY.MRQ.TPLKKV.LDMRTNTICWNPMEAFIFT.ANED.NL
Retrocopy WRFDSISSIKFNPIETFLLESCASDRNIVLYAMRQGTPLKKVALDMRTNTICWNPMEAFIFTVANEDNNL

Parental  YTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPIDKSRSREVYHTKRMQHVICVKW
          .TFDMRALDT.VMVHM.HVS.VLDVDYSPTGKEF.SASFDKSI.IF..DKS.SR..YHTKRMQHV.CVK.
Retrocopy LTFDMRALDTSVMVHMNHVSSVLDVDYSPTGKEFMSASFDKSI*IFTVDKSQSRVAYHTKRMQHVVCVKR

Parental  TSDSKYIMCGSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHHPHIKRIARHRHLPKSIYSQ
          TSDSKYIM.GSDEMNI.L.KANASE.LGVLTS.EKAAK.Y.QKLKEK.QHHPHIK.IARH.HLPKSIYS.
Retrocopy TSDSKYIMYGSDEMNIHLCKANASEELGVLTS*EKAAKYYSQKLKEKCQHHPHIKQIARHQHLPKSIYSP

Parental  IQEQRIMKEA
          IQEQ.IMKEA
Retrocopy IQEQCIMKEA

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	12.74 RPM
SRP051959_heart	0.09 RPM	8.31 RPM
SRP051959_kidney	0.00 RPM	12.18 RPM
SRP051959_liver	0.09 RPM	10.94 RPM
SRP051959_lung	0.00 RPM	11.96 RPM
SRP051959_lymph_node	0.00 RPM	14.36 RPM
SRP051959_skeletal_muscle	0.48 RPM	6.73 RPM
SRP051959_spleen	0.04 RPM	16.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3083 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3083 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083 , retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,