RetrogeneDB ID: retro_cjac_3027

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:129898999..129899890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000031235
• Aliases: None
• Description: None

Sequence

>retro_cjac_3027
GCCCGCGCCGCCGCCGCCTTCGGAGCGCAGGGTCTCGCCGCAGCAGCTGCTCGCAGCTCTCGGGGGATCTAATAGGGAGG
CCTGTGGGCGCACGGGCGAGTGGGCCAGGACCCGGAGCGGTTGAGGAGCCGGCAGCAGCAGCGCGGCGAGCCCCGGACGA
GGCGATCCGCGCTCCTGAAAACTCGGGCGCGCGCTCGCGCCGCTGCACCCGCATCGATGAAGATGGTCGCGCCCTGGACG
CGGTTCTACTCCAACAGCTGCTGCCTGTGCTGCCATGTCCGCACCGGCACCATCCTGCTCGGTGTCTGGTACCTGGTCAT
CAATGCCGTGGTACTGTTGATTTTATTGAGTGCCCTGGCTGACCCGGATCAGTATCACTTTTCAAGTTCTGAACTGGGCG
GTGACTTTGAGTTCATGGATGATGCCAACATGTGCATTGCCATTGCGATTTCTGTTCTCATGATTCTGATATGTGCTATG
GCTACTTACGGAGCATACAAGCAACACGTAGCCTGGATTATCCCATTCTTCTGTTACCAGATCTTTGATTTTGCCCTGAA
CCCCTTGGTTGCAATCACTGTGTTTGTTTATCCAAACTCCATTCAGGAATACATACGACAACTGCCTCCTAATTTTCCCT
ACAGAGATGATGTCATGTCAGTGAATCCTACCTGTTTGGTCCTTATTATTCTTCTGTTTATTAGCATTATCTTGACTTTC
AAGGGTTACTTGATTAGTTGTGTTTGGAACTGATACCTATACATAAATGGCAGGAACTCCTCCGATGTCCTGGTTTACGT
TACCAGCAATGACAATAAGGTGCTGCTACCCCCGTATGATGAGGCCACTGTGAATGGTGCTGCCAAACAGCCGCCGCCCC
CTTACGTGTCT

Alignment

ORF - retro_cjac_3027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.26 %
• Parental protein coverage: 85.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRARVTWPAQGLAAAAARSSRGIEEGGLWAHGRVGRDPERLRSRQQQRGEPRTRRSALLKTWACARAAAP
          .RA.....AQGLAAAAARSSRGI..GGLWAHGRVG.DPERLRSRQQQRGEPRTRRSALLKT.A.ARAAAP
Retrocopy ARAAAAFGAQGLAAAAARSSRGI**GGLWAHGRVGQDPERLRSRQQQRGEPRTRRSALLKTRARARAAAP

Parental  AAMKMVAPWTRFYSNSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPDQYRFSSSELGGDFEFMD
          A.MKMVAPWTRFYSNSCCLCCHVRTGTILLGVWYL.INAVVLLILLSALADPDQY.FSSSELGGDFEFMD
Retrocopy ASMKMVAPWTRFYSNSCCLCCHVRTGTILLGVWYLVINAVVLLILLSALADPDQYHFSSSELGGDFEFMD

Parental  DANMCIAIAISVLMILICAMATYGAYKQHAAWIIPFFCYQIFDFALNTLVAITVLVYPNSIQEYIRQLPP
          DANMCIAIAISVLMILICAMATYGAYKQH.AWIIPFFCYQIFDFALN.LVAITV.VYPNSIQEYIRQLPP
Retrocopy DANMCIAIAISVLMILICAMATYGAYKQHVAWIIPFFCYQIFDFALNPLVAITVFVYPNSIQEYIRQLPP

Parental  NFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDNTVLLPPYD
          NFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISCVWN.Y.YINGRNSSDVLVYVTSNDN.VLLPPYD
Retrocopy NFPYRDDVMSVNPTCLVLIILLFISIILTFKGYLISCVWN*YLYINGRNSSDVLVYVTSNDNKVLLPPYD

Parental  EATGNGAAKEPPPPYLS
          EAT.NGAAK.PPPPY.S
Retrocopy EATVNGAAKQPPPPYVS

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	0.20 RPM	7.37 RPM
SRP051959_heart	0.18 RPM	30.17 RPM
SRP051959_kidney	0.13 RPM	5.32 RPM
SRP051959_liver	0.02 RPM	2.53 RPM
SRP051959_lung	0.42 RPM	5.64 RPM
SRP051959_lymph_node	0.53 RPM	1.05 RPM
SRP051959_skeletal_muscle	0.09 RPM	2.03 RPM
SRP051959_spleen	0.21 RPM	4.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3027 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3027 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027 ,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76,