RetrogeneDB ID: retro_cjac_396

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:55542843..55543451(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016303
• Aliases: None
• Description: None

Sequence

>retro_cjac_396
GAGCGCCGCGTCCCCTTCTTGCTCCTGCGGAGCCGCAGCTGGGACCCCTTCCGCGACTGGTACCCGCACAGCTGTCTCTT
CGACCAGGCCTTCGGGATGCCCCGGCTGCCCGAGGAGTGCTAGCAGTGGTTCGGCACCAGCAGCTGGCCGGGCTACGTGC
GCCCCCTGCCCCCCGCCGCGGTGGAGGGCCCCCGGTGGCCGTGCCTGCCTACAGCCTCAAGCTCAGCCGGCAGCTCAACA
GTGGGGTCTCAGAGATCCGGCACACTGCGGACCACTGGCGCGTGTCCCTGGACGTCAACCACTTTGCCCCCGAGAAGCTG
ACGGTCAAGACCAAGGATGGCGTGGTGGAGATCACTGGCAAGCACGAGAAGCGGCAGGATTAGCACGGATTCATCTCCAG
CTGCTTCACCCGGAAATACACACTGCCCCCTGGTGTGGACCCCACTCAGGTCTCCTCCTCCCTGTCCCCTGAGGGCACAC
TGACCGTGGAGGCCCCCATGCCCAAGTCAGCCACGCAGTCCAAGGAGATCACCATCCCCGTCACCTTCAAGTCGCGGGCC
CAGCTTGGGGGCCCAGAAGCTGCAAAATCCGACCAGTCTGCAGCCAAG

Alignment

ORF - retro_cjac_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERRVPFSLLRSPSWDPFRDWYPHNRLFDQAFGMPRLPEEWSQWFGTSSWPGYVRPLPPAAVEGPA-VAAP
          ERRVPF.LLRS.SWDPFRDWYPH..LFDQAFGMPRLPEE..QWFGTSSWPGYVRPLPPAAVEGP..VA.P
Retrocopy ERRVPFLLLRSRSWDPFRDWYPHSCLFDQAFGMPRLPEEC*QWFGTSSWPGYVRPLPPAAVEGPR<VAVP

Parental  AYSRALSRQLSSGVSEIRHTADRWRVSLDVNHFAPEELTVKTKDGVVEITGKHEERQDEHGFISRCFTRK
          AYS..LSRQL.SGVSEIRHTAD.WRVSLDVNHFAPE.LTVKTKDGVVEITGKHE.RQD.HGFIS.CFTRK
Retrocopy AYSLKLSRQLNSGVSEIRHTADHWRVSLDVNHFAPEKLTVKTKDGVVEITGKHEKRQD*HGFISSCFTRK

Parental  YSLPPGVDPTQVSSSLSPEGTLTVEAPMPKPATQSNEITIPVTFESRAQLGGPEAAKSDQSAAK
          Y.LPPGVDPTQVSSSLSPEGTLTVEAPMPK.ATQS.EITIPVTF.SRAQLGGPEAAKSDQSAAK
Retrocopy YTLPPGVDPTQVSSSLSPEGTLTVEAPMPKSATQSKEITIPVTFKSRAQLGGPEAAKSDQSAAK

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	12.34 RPM
SRP051959_heart	0.00 RPM	33.62 RPM
SRP051959_kidney	0.02 RPM	13.11 RPM
SRP051959_liver	0.00 RPM	10.61 RPM
SRP051959_lung	0.00 RPM	11.19 RPM
SRP051959_lymph_node	0.07 RPM	10.48 RPM
SRP051959_skeletal_muscle	0.07 RPM	117.86 RPM
SRP051959_spleen	0.06 RPM	16.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_396 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016303	5 retrocopies	retro_cjac_1914, retro_cjac_2499, retro_cjac_396 , retro_cjac_412, retro_cjac_591,
Homo sapiens	ENSG00000106211	1 retrocopy	retro_hsap_4830,
Gorilla gorilla	ENSGGOG00000002700	1 retrocopy	retro_ggor_3012,
Mus musculus	ENSMUSG00000004951	1 retrocopy	retro_mmus_1097,
Pongo abelii	ENSPPYG00000029733	1 retrocopy	retro_pabe_3755,