RetrogeneDB ID: retro_cjac_2962

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:9152298..9152655(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005579
• Aliases: None
• Description: None

Sequence

>retro_cjac_2962
GTTCATATTGTCTCACTCAGCATCCCCTCTTCGACGTCCTCATTGCTTAGACCTTAGCTAATGCCGTACATAACCTAGGG
ATGAATGGATTTTTGTGTGCCTGTAAGGGACACCTTTAGAAACTCCTGACCAGGGTAAAGCAGGGCTCCCAACGCACGGA
GAACAACTGGAGGATGGAATACCGTCTGCATCTTCACGGAAGTTTCCCACCATCTCTCCAATAATTCTGTATTTTCCAGC
AAGTTTCTATAGAAGTATAATCCAACCCGCACCATCCTAAGCACAGCTTCTCTCCCGAGTATGCTAACTCTCCAAATGCC
ACGACGACATGGTGTTCCAATCTTTGGAATTAATAAG

Alignment

ORF - retro_cjac_2962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 78.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LHIVLLSIP-FFSVPVAWTLTNIIHNLGMYVFLHAVKG-TPFETPDQGKARLLTHWEQLDYGVQFTSSRK
          .HIV.LSIP..F.V..A.TL.N..HNLGM..FL.A.KG.TP.ETPDQGKA.L.TH.EQL..G....SSRK
Retrocopy VHIVSLSIP<LFDVLIA*TLANAVHNLGMNGFLCACKG<TPLETPDQGKAGLPTHGEQLEDGIPSASSRK

Parental  FFTISPIILYFLASFYT-KYDSTHFILNTASLLSVLIPKMPQLHGVRIFGINK
          F.TISPIILYF.ASFY..KY..T..IL.TASL.S.L...MP..HGV.IFGINK
Retrocopy FPTISPIILYFPASFYR<KYNPTRTILSTASLPSMLTLQMPRRHGVPIFGINK

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	12.14 RPM
SRP051959_heart	0.02 RPM	17.98 RPM
SRP051959_kidney	0.00 RPM	16.06 RPM
SRP051959_liver	0.00 RPM	17.59 RPM
SRP051959_lung	0.10 RPM	14.01 RPM
SRP051959_lymph_node	0.00 RPM	16.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.77 RPM
SRP051959_spleen	0.00 RPM	18.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2962 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005579	1 retrocopy	retro_cjac_2962 ,
Homo sapiens	ENSG00000128699	1 retrocopy	retro_hsap_645,
Gorilla gorilla	ENSGGOG00000015259	1 retrocopy	retro_ggor_565,
Loxodonta africana	ENSLAFG00000007769	1 retrocopy	retro_lafr_411,
Myotis lucifugus	ENSMLUG00000014339	1 retrocopy	retro_mluc_2318,
Macaca mulatta	ENSMMUG00000014316	1 retrocopy	retro_mmul_2432,
Nomascus leucogenys	ENSNLEG00000006625	1 retrocopy	retro_nleu_730,
Pongo abelii	ENSPPYG00000013017	2 retrocopies	retro_pabe_570, retro_pabe_571,
Pan troglodytes	ENSPTRG00000012736	1 retrocopy	retro_ptro_469,
Sus scrofa	ENSSSCG00000016044	1 retrocopy	retro_sscr_247,
Tupaia belangeri	ENSTBEG00000012942	1 retrocopy	retro_tbel_10,
Tursiops truncatus	ENSTTRG00000005240	2 retrocopies	retro_ttru_1846, retro_ttru_770,