RetrogeneDB ID: retro_cjac_2381

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:139948138..139948969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSCJAG00000035699
• Aliases: None
• Description: None

Sequence

>retro_cjac_2381
CAAGGTCTTTGCCTTCCTTATGAAGACTGTGTTGATCAGGCCGTTCAGTTTTGTGTTCAGGCTCTCAGAATGACTCCTGA
CCATAAGAAGCCTTGCCTTGCTTGCAGAAATGCCAGACCACTTAACACAAAGAAAGAAGACTGGAATAAAGCATTTAGGG
AAAGACATTACAAACTAGCTGATGAACTGTACCCAGAAACCCCAGGATAGACCCCCGACAACATAAAAACAATTGCCTAA
CTCTACTGTAACCAGGATACGGTTAATTCCAAGCTTAGGAAACTAGATGACGCAATAGACGGCTGCACAAATGCAGCGAA
GCTCACAACACTTATTTAAACGCCTGTTTGAGAAGAGCTCAGTGTTCCATGGACACAGAACAGTATGAAGAAACAGTGCG
AGACTATGGAAACGTATGTCAGATGAGGAAAACAAAAGAATGCAAATAGCTCCTAAAAAATGCACAGGTGGAACTGAGGA
AAGAGTAAGAGGGAAAATTACTGCAAGGTTCTGGGAGTGGACAAGAATGCCTCTGAGGACAAGATCAAGAAAGCATATTG
GAAACAGGCCTTGATGCACCATCCACATCAAGCACTGGTGGGGCCAGTGCTGGGGTCCAGAAGGAGGAGAAGATCAAGGA
AGCGGCAAGGTCTTTACCATCCTCTTTGATCCCAAGAAAATGGCTCATTATCACAGTGGATAGGACCTGATAAGGAGGAC
ATGAAATTGGGTGATTTTGATGCAAACAGTATCTTCAAGGTATTCTTTCACGGTCCTGGGGGCTTCAGCTTTGAAGCATC
TGGTCCAAGGAGTTTCTTTCTTCAATTTGGC

Alignment

ORF - retro_cjac_2381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.25 %
• Parental protein coverage: 63.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGLCLYYEDCIEKAVQFFVQALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEALGI
          .GLCL.YEDC...AVQF.VQALRM.PDH.K.C.ACRNA..L..KKED.NKAF.E..YKLA.ELY.E..G.
Retrocopy QGLCLPYEDCVDQAVQFCVQALRMTPDHKKPCLACRNARPLNTKKEDWNKAFRERHYKLADELYPETPG*

Parental  DPNNIKTNAKLYCNRGTVNSKLRKLDDAIEDCTNAVKL-DDTYIKAYLRRAQCYMDTEQYEEAVRDYEKV
          .P.NIKT.A.LYCN..TVNSKLRKLDDAI..CTNA.KL...TY..A.LRRAQC.MDTEQYEE.VRDY..V
Retrocopy TPDNIKTIA*LYCNQDTVNSKLRKLDDAIDGCTNAAKL<HNTYLNACLRRAQCSMDTEQYEETVRDYGNV

Parental  YQTEKTKEHKQLLKNAQLELK-KSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDR-HSGASAEVQK
          .Q..KTKE.K.LLKNAQ.EL..KSKR..Y.K.LGVDKNASED.IKKAY.K.ALMHHP.....G.......
Retrocopy CQMRKTKECK*LLKNAQVELR>KSKRENYCKVLGVDKNASEDKIKKAYWKQALMHHPHQ<STGGASAGVQ

Parental  EEEKKFKEV-GEAFTILSDPKKKTRYDSGQDL-DEEGMNMGDFDANNIFKAFFGGPGGFSFEASGPGNFF
          .EE.K.KE..G..FTIL.DPKK...Y.SG.DL.D.E.M..GDFDAN.IFK.FF.GPGGFSFEASGP..FF
Retrocopy KEE-KIKEA<GKVFTILFDPKKMAHYHSG*DL<DKEDMKLGDFDANSIFKVFFHGPGGFSFEASGPRSFF

Parental  FQFG
          .QFG
Retrocopy LQFG

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	21.57 RPM
SRP051959_heart	0.00 RPM	22.03 RPM
SRP051959_kidney	0.00 RPM	29.57 RPM
SRP051959_liver	0.00 RPM	20.97 RPM
SRP051959_lung	0.00 RPM	27.20 RPM
SRP051959_lymph_node	0.00 RPM	27.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.88 RPM
SRP051959_spleen	0.00 RPM	27.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2381 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2381 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381 , retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,