RetrogeneDB ID: retro_cjac_612

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:128199479..128200382(-)
• 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_612
GAAGAGGAAGAACCATTACATACAATATTAGGAAAGGCAGTGTGGACTGGGATTGCCCATCACTGTAAAGAAGCTGTTTT
TGCTACACGTGCACAGCAAATAGACATTTGGGATAAACAAAGAACTAATCCTATATGTTCAATGACCTGGGAATTTGACA
GTATGAGTAGTGTTAAATTTAACCCAATTGAGACATTTCTTTTGGAAAGTTGTGTGCCTGACAGGAATATAGTACTATAT
GATAGGAGGCAAGCTACTCCTTTGAAAAAGGTTATCTTAGACAGGAGAACAAATACAATCTGTTGGAACCCTATGGAAGC
TTTCATTTTTACAGCGACAAATGCAGATTCTAATTTATATACTTTTAAGATGTGTGCAGTGGACACTCCTGTAATGGTCC
ATATGGATCATGTATCTGCATTCCTTGATGTGGATTACTCTCCCACTAGGAAAGAGTTTGTGTCTGCTAGTTTTGATAAA
TCTATTCAAATCTTTCCTGTGGACAAAAGTTGAAGCAGGGAGGTATATCATACAAAGCGAACACAACATGTTATCTGTGT
AAAATGGACTTCTGACTGCAAGTATATTATGTTTGGGTCTGATGAAATGAACATTCGCCTATGGCAAGCTAATGCTTCTG
AAAAATTGGGTGTGCTTACGTCACGAGAAAACGCAGCCAAGGATTATAACCAGAAATTGAAGGAAAAATTTCAGCATCAT
CCTCATATAAAACATATAGCTCGTGATTGACATCTACCAAAATCTATCTACAGCCATATTCAGGAACAGCACATCATGAA
AGAAGCTTGTCGATGAAAGGAAGTGAATCATATTAAACACGGCAAGCCTGGATCTGTGCCAGTTGTGTCAGAGAAGAAGA
AACACGTAGTGGCAGTTGTAAAA

Alignment

ORF - retro_cjac_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.38 %
• Parental protein coverage: 67.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPICSMTWGFDSISSVKFNPIETFLLGS
          EEEEPLHTILGK.V.TGI.HH.KEAVFAT..QQ.DIWD.QRTNPICSMTW.FDS.SSVKFNPIETFLL.S
Retrocopy EEEEPLHTILGKAVWTGIAHHCKEAVFATRAQQIDIWDKQRTNPICSMTWEFDSMSSVKFNPIETFLLES

Parental  CASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRALDTPVMVHMDHVSA
          C..DRNIVLYD.RQATPLKKVILD.RTNTICWNPMEAFIFTA.N.D.NLYTF.M.A.DTPVMVHMDHVSA
Retrocopy CVPDRNIVLYDRRQATPLKKVILDRRTNTICWNPMEAFIFTATNADSNLYTFKMCAVDTPVMVHMDHVSA

Parental  VLDVDYSPTGKEFVSASFDKSIRIFPIDKSRSREVYHTKRMQHVICVKWTSDSKYIMCGSDEMNIRLWKA
          .LDVDYSPT.KEFVSASFDKSI.IFP.DKS.SREVYHTKR.QHVICVKWTSD.KYIM.GSDEMNIRLW.A
Retrocopy FLDVDYSPTRKEFVSASFDKSIQIFPVDKS*SREVYHTKRTQHVICVKWTSDCKYIMFGSDEMNIRLWQA

Parental  NASEKLGVLTSREKAAKDYNQKLKEKFQHHPHIKRIARHRHLPKSIYSQIQEQRIMKEARRRKEMNRIKH
          NASEKLGVLTSRE.AAKDYNQKLKEKFQHHPHIK.IAR..HLPKSIYS.IQEQ.IMKEA.R.KE.N.IKH
Retrocopy NASEKLGVLTSRENAAKDYNQKLKEKFQHHPHIKHIARD*HLPKSIYSHIQEQHIMKEACR*KEVNHIKH

Parental  SKPGSVPVVSEKKKHVVAVVK
          .KPGSVPVVSEKKKHVVAVVK
Retrocopy GKPGSVPVVSEKKKHVVAVVK

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	0.02 RPM	12.74 RPM
SRP051959_heart	0.00 RPM	8.31 RPM
SRP051959_kidney	0.13 RPM	12.18 RPM
SRP051959_liver	0.00 RPM	10.94 RPM
SRP051959_lung	0.02 RPM	11.96 RPM
SRP051959_lymph_node	0.00 RPM	14.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.73 RPM
SRP051959_spleen	0.02 RPM	16.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_612 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_612 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,