RetrogeneDB ID: retro_cjac_2693

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:15898913..15899651(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001823
• Aliases: None
• Description: None

Sequence

>retro_cjac_2693
AAGAAGGTAGATCATGACTATAATGCCCTTCAAGAAAGACTCAACACCTTGCCTGAGAAATTGTCTCACAATATAATGGT
ACCGTTCGGCCCTTTCGCCTTCATGCCCGGAAAACTTGTCCCTACTGTTGAAGTCACTGTTTTACTGGGGGACAACTGGT
TTGCAAAGTGCTCAGCAAAGCAGGCTGTAGGTTCAGTTGAGCACCGGAAGGAACGTGTAAGAAAAACAATAGAGGATTTA
AGAAAAGGGGTGAAAAATTTTGAATCAGGAGTTGAATTCACAGAAGATTTGCAGAAAATGAGTGATGCTGAAGGTGATAT
TGTTGATATAAGAGAAGAAATTAAATGTGACTTTGAATTTAAAGCAAAACACCGAGTTGCTCATAAACCACATTCCAAAC
CAAAAACTTCAGATATTTTTGAAGCAGATATTGCAAATGACATGAAATCCAAGGATTTCCCTGCTGATAAAGAACTGTGG
GCTCGACTTGAAGAACTAGAGAGATAAGAAGAATTGCTGGGTGAACTTGATAGTAAGCCTGATACTGCAAATGGAGAAGA
TACGACATCTTCTGAAGAAGAAAAGAAAGATCACAACACAAATGTGAATGTTATGCATCAAGTAACAGACTCTCATACTC
CGGACAGTTGTCATAAGCATGTGTCAAGTTCAGAACCATTTAGGGATCAGCTGAATAGTCAGTTGAACTGTTCGGTGAAT
GGTTCCAGTTCTTACCAC

Alignment

ORF - retro_cjac_2693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 52.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKVDNDYNALRERLNTLPDKLSYNIMVPFGPFAFMPGKLVHTNEVTVLLGDNWFAKCSAKQAVGLVEHRK
          KKVD.DYNAL.ERLNTLP.KLS.NIMVPFGPFAFMPGKLV.T.EVTVLLGDNWFAKCSAKQAVG.VEHRK
Retrocopy KKVDHDYNALQERLNTLPEKLSHNIMVPFGPFAFMPGKLVPTVEVTVLLGDNWFAKCSAKQAVGSVEHRK

Parental  EHVRKTIEDLRKVVKNFESRVEFTEDLQKMSDAAGDIVDIREEIKCDFEFKAKHRVAHKPHSKPKTSDIF
          E.VRKTIEDLRK.VKNFES.VEFTEDLQKMSDA.GDIVDIREEIKCDFEFKAKHRVAHKPHSKPKTSDIF
Retrocopy ERVRKTIEDLRKGVKNFESGVEFTEDLQKMSDAEGDIVDIREEIKCDFEFKAKHRVAHKPHSKPKTSDIF

Parental  EAGIANDMKSKDLLADKELWARLEELERQEELLGELDSKPDTVTVNGEDTTSSEEEKEDHNTNVNVMHQV
          EA.IANDMKSKD..ADKELWARLEELER.EELLGELDSKPD..T.NGEDTTSSEEEK.DHNTNVNVMHQV
Retrocopy EADIANDMKSKDFPADKELWARLEELER*EELLGELDSKPD--TANGEDTTSSEEEKKDHNTNVNVMHQV

Parental  TDSHTPDSCHKHVASSEPFSDQLNSQLNCSVNGSSSYH
          TDSHTPDSCHKHV.SSEPF.DQLNSQLNCSVNGSSSYH
Retrocopy TDSHTPDSCHKHVSSSEPFRDQLNSQLNCSVNGSSSYH

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	0.11 RPM	24.54 RPM
SRP051959_heart	0.05 RPM	28.40 RPM
SRP051959_kidney	0.07 RPM	37.05 RPM
SRP051959_liver	0.09 RPM	23.89 RPM
SRP051959_lung	0.05 RPM	37.22 RPM
SRP051959_lymph_node	0.09 RPM	48.67 RPM
SRP051959_skeletal_muscle	0.02 RPM	17.19 RPM
SRP051959_spleen	0.11 RPM	32.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2693 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2693 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001823	1 retrocopy	retro_cjac_2693 ,
Monodelphis domestica	ENSMODG00000012675	1 retrocopy	retro_mdom_1513,
Pongo abelii	ENSPPYG00000009810	1 retrocopy	retro_pabe_547,
Pan troglodytes	ENSPTRG00000010784	1 retrocopy	retro_ptro_3086,