RetrogeneDB ID: retro_cjac_2465

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:111097169..111097612(-)
• Located in intron of: ENSCJAG00000005032

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC117
• Ensembl ID: ENSCJAG00000020088
• Aliases: None
• Description: coiled-coil domain containing 117 [Source:HGNC Symbol;Acc:26599]

Sequence

>retro_cjac_2465
AAAAAAAGGCTAACCGAAGCAGAGCCCTATGCTGGTTCTAATGACTAGATTATTTTTGCACATCAAGATGGAGAGGGTCA
TGTAGTAGATCTCTGCACTAGTGGCCTTTTTGTACCTGCAATGTAAGATGTTATATGTGAAAAAATGGATCAGATGACAG
GAGAACAACTATGAAATTGCCAGAAGGAAGCTTTAGATTAAAAGGACAGGATAATTGACTAAGATGAAGAAGTTGAAGCT
GACAGAAATGTTAACCATCTCCCCAGTCTTGCCCTTTCTGATATCATGAAAACAGATTCAAAGAATAATTTGATGAGCTG
TTAACAAATAAAATAATTGAGTCCATGAGCTGTTCTTCCATGTAGCTTTTTCTTTGGAAACCTTCCCCTGAACTTTCCAA
TAAGCCAAAGCCATCCTCTAATGCTAAAAAAACTGCACAGGAG

Alignment

ORF - retro_cjac_2465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.24 %
• Parental protein coverage: 57.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKRITEAELCARPNDWILCAHQDVEGHGVNPCTSGLSVPGILDVICEEMDQTTGEPQCEAARRKLQEIED
          KKR.TEAE..A..ND.I..AHQD.EGH.V..CTSGL.VP...DVICE.MDQ.TGE.Q............D
Retrocopy KKRLTEAEPYAGSND*IIFAHQDGEGHVVDLCTSGLFVPAM*DVICEKMDQMTGE-QL*NCQKEALD*KD

Parental  RIIDEDEEVEAVRNVNHLPSLVLSDTMKTGLKRE-FDEVFTKKIIESMSRPSMELVLWKPLPELLSDKPK
          RIID.DEEVEA.RNVNHLPSL.LSD.MKT..K...FDE..T.KIIESMS..SM.L.LWKP.PE.LS.KPK
Retrocopy RIID*DEEVEADRNVNHLPSLALSDIMKTDSKNN<FDELLTNKIIESMSCSSM*LFLWKPSPE-LSNKPK

Parental  PSSNAKNYTGE
          PSSNAK....E
Retrocopy PSSNAKKTAQE

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	0.38 RPM	9.01 RPM
SRP051959_heart	0.19 RPM	7.95 RPM
SRP051959_kidney	0.20 RPM	12.62 RPM
SRP051959_liver	0.11 RPM	18.91 RPM
SRP051959_lung	0.31 RPM	11.47 RPM
SRP051959_lymph_node	0.37 RPM	14.57 RPM
SRP051959_skeletal_muscle	0.17 RPM	9.61 RPM
SRP051959_spleen	0.42 RPM	17.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2465 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2465 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020088	1 retrocopy	retro_cjac_2465 ,
Microcebus murinus	ENSMICG00000004228	2 retrocopies	retro_mmur_431, retro_mmur_914,
Macaca mulatta	ENSMMUG00000007214	1 retrocopy	retro_mmul_2580,
Tursiops truncatus	ENSTTRG00000011845	1 retrocopy	retro_ttru_1174,