RetrogeneDB ID: retro_cjac_4152

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:40202790..40203183(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHISA5
• Ensembl ID: ENSCJAG00000002915
• Aliases: None
• Description: shisa homolog 5 (Xenopus laevis) [Source:HGNC Symbol;Acc:30376]

Sequence

>retro_cjac_4152
GGGTTCAGCACAACAGTGGCCATCAGCCTGACCATCTTTGTGCTGTCTGTTGTCACTATCATCATCTGCTTCACCTGTTC
CTGCTGCTCCCTCTACAAGATGTGAGGCCGACTGTGTCCAGTTGTGACCACCACCATGTCCACTACTGTGGTGCATGCCC
CTTACCCTCAGCATCCAAGTGTGAGGCTCAGCTACCCTGGACCAAGCTACCAGGGCTACCACCCCATGTCCTCCCCAGCC
AGCGATGCCAGCAGCACCCTACCCAAAACAGTACCCACCACCTTACCTGGCCTGCTGTCCTACCACGAGACCCTGGCTGG
AGGAACAGCTGCACCCTATCCCACCAGCCAGCCTCCTTCCAACCCGGCCTACATGGATGCCCCAAAGGCGGCC

Alignment

ORF - retro_cjac_4152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 55.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCCQPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSY
          GF..T.A..LTIFVLSVVTIIICFTCSCC.LYK......PVVTTT.STTVVHAPYPQ.PSV..SYPGPSY
Retrocopy GFSTTVAISLTIFVLSVVTIIICFTCSCCSLYKM*GRLCPVVTTTMSTTVVHAPYPQHPSVRLSYPGPSY

Parental  QGYHAM-PPQPGMPAAPYPMQYPPPYPAQPM-GPPACHETLAGGVAAPYSASQPPYNPAYMDAPKAA
          QGYH.M.PPQP.MPAAP....YP..YP.....G....HETLAGG.AAPY..SQPP.NPAYMDAPKAA
Retrocopy QGYHPM>PPQPAMPAAP----YPKQYPPPYL<GLLSYHETLAGGTAAPYPTSQPPSNPAYMDAPKAA

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	7.34 RPM
SRP051959_heart	0.00 RPM	5.44 RPM
SRP051959_kidney	0.00 RPM	14.73 RPM
SRP051959_liver	0.00 RPM	8.97 RPM
SRP051959_lung	0.00 RPM	24.81 RPM
SRP051959_lymph_node	0.00 RPM	30.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.73 RPM
SRP051959_spleen	0.00 RPM	13.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4152 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4152 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4812
Gorilla gorilla	retro_ggor_2996
Macaca mulatta	retro_mmul_2565

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077, retro_cjac_4152 ,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996, retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,