RetrogeneDB ID: retro_cjac_1575

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:70896077..70896957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF620
• Ensembl ID: ENSCJAG00000017904
• Aliases: None
• Description: zinc finger protein 620 [Source:HGNC Symbol;Acc:28742]

Sequence

>retro_cjac_1575
AGTGTCAGCACACATCTCATTACAAAGCAGGACTTTGCTGAAGAACGGGTGTTTTATAAATGTAGCGAGTGTGGCAGTTA
CTACAACCCACATTCAGACTTTCACCAGCATCAGACAATTCACACTAGTGAAAAGCCCTACAAATGCAAAGAATGTGGGA
GAACCTTCAGATATAACTCAAAACTGTCACGGCATCAGAAAATCCACACTGGAGAGAAACCATATTCATGTGAGGAATGC
GGACAAGCCTTCAGTCAAAATTCCCACCTTCTTCAGCATCAGAAACTCAATGGTGGACAGAGGCCCTATGAATGTGCTGA
CTGTGGAAAAACCTTCAGCTATAATTCAAAACCGATTCGGCATCAGAGAATCCATACTGGGGAGAAGCCCTTTAAATGTA
AGGAATGTGGGAAGGCCTTCAGGTGTAGCTATGACTGCTTCATCCATGAATGAATTCGCACTGGGGAGAAGCCCTATGAA
TGTAAGGAGTGCGGGAAGAGTTTTGAGTTCTAATACAGTCCTGATTCAGCATCAGAGAATGCACACTGGGGAGAAACCTT
ATGAATGTAAAGAGTGTGGCAAGGCCTTCCACCGCAGTTCGGTGTTTCTTCAGCACCAGAGGTTCCACACTGGGGAACAA
CTCTACAAATGTAACGAATGTTGGAAAACTTTCAGTTGTGGCTCCTGCTTCATAGTGCATCGGAGAATCCACACCGGGAA
GAAGCCCTAGGAATGCCAGGAATGTGGGAAGACATTCAGTCAGAAGATCACTCTGGTTCAGCATCAGCGAGTTCACACTG
GGGAGAAAGCTTTTGAGTGTAAGGAGTGCGGGAAAACCTTCAAATGGAATGCAAGTTTCATTCAGCATCAGAAGTGGCAT

Alignment

ORF - retro_cjac_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.22 %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSSVFLQHQRFHTGEKLYECHECWKTFSCSSSFTVHQRMHTGEKPFECKECGKRLSSNTALTQHQRIHT
          S.S......Q.F......Y.C.EC.......S.F..HQ..HT.EKP..CKECG.....N..L..HQ.IHT
Retrocopy SVSTHLITKQDFAEERVFYKCSECGSYYNPHSDFHQHQTIHTSEKPYKCKECGRTFRYNSKLSRHQKIHT

Parental  GEKPFECKECGKAFNQKITLVQHQRVHTGEKPYECKVCGKNFSWKGSLIRHQMSHTGEKPFKCKECGKAF
          GEKP..C.ECG.AF.Q...L.QHQ....G..PYEC..CGK.FS.....IRHQ..HTGEKPFKCKECGKAF
Retrocopy GEKPYSCEECGQAFSQNSHLLQHQKLNGGQRPYECADCGKTFSYNSKPIRHQRIHTGEKPFKCKECGKAF

Parental  KSSYDCIVHEKNHVGEGPYECKECGKG-LSSSTALTQHQRIHTGEKPYDCKECGKAFRRSTTYLQHQRLH
          ..SYDC..HE....GE.PYECKECGK..LSS.T.L.QHQR.HTGEKPY.CKECGKAF.RS...LQHQR.H
Retrocopy RCSYDCFIHE*IRTGEKPYECKECGKS>LSSNTVLIQHQRMHTGEKPYECKECGKAFHRSSVFLQHQRFH

Parental  TGEKLYQCKECWKAFGCRSLFIVHQRIHTGEKPYQCKECGKAFTQKKASIQHQRVHTAEKPYECKVCGKA
          TGE.LY.C.ECWK.F.C.S.FIVH.RIHTG.KP..C.ECGK.F.QK....QHQRVHT.EK..ECK.CGK.
Retrocopy TGEQLYKCNECWKTFSCGSCFIVHRRIHTGKKP*ECQECGKTFSQKITLVQHQRVHTGEKAFECKECGKT

Parental  FKWYGSFVQHQKLH
          FKW..SF.QHQK.H
Retrocopy FKWNASFIQHQKWH

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	0.33 RPM	7.14 RPM
SRP051959_heart	0.21 RPM	8.10 RPM
SRP051959_kidney	0.24 RPM	11.05 RPM
SRP051959_liver	0.17 RPM	8.66 RPM
SRP051959_lung	0.39 RPM	11.18 RPM
SRP051959_lymph_node	0.82 RPM	13.42 RPM
SRP051959_skeletal_muscle	0.11 RPM	6.49 RPM
SRP051959_spleen	0.42 RPM	11.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1575 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017904	1 retrocopy	retro_cjac_1575 ,