RetrogeneDB ID: retro_cjac_1771

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:35158338..35158625(+)
• Located in intron of: ENSCJAG00000006466

Retrocopy information

• Ensembl ID: ENSCJAG00000006472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPZ1
• Ensembl ID: ENSCJAG00000018887
• Aliases: None
• Description: coatomer protein complex, subunit zeta 1 [Source:HGNC Symbol;Acc:2243]

Sequence

>retro_cjac_1771
GCAGCTTATGAAAATGAGCTGATGCTTATGGCTGTTCTGAACTGCCTCTTCGACTCATTGAGACAGATACTGAGGAAAAA
TGTAGAAAAGCGAGCACTACTGGAGAACATGGAGGGGCTGTTCTTGGCTGTGAATGAAACTGTAGATGGAGGGTGATCCT
AGAGAGTGATCCCCAGCAGGTGGTACATCCGGTGGCATTAAGGGGTGAAGATGTCCCCCTTACCGAGCAAACCATGTCTC
AGGTGCTACAGTCAGCCAAAGAACAGATCAAGTGGTCGCTCCTTCAG

Alignment

ORF - retro_cjac_1771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 54.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGG-VILESDPQQVVHRVALRG
          ..YENELMLMAVLNCLFDSL.Q.LRKNVEKRALLENMEGLFLAV.E.VDGG.VILESDPQQVVH.VALRG
Retrocopy AAYENELMLMAVLNCLFDSLRQILRKNVEKRALLENMEGLFLAVNETVDGG<VILESDPQQVVHPVALRG

Parental  EDVPLTEQTVSQVLQSAKEQIKWSLLR
          EDVPLTEQT.SQVLQSAKEQIKWSLL.
Retrocopy EDVPLTEQTMSQVLQSAKEQIKWSLLQ

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	0.16 RPM	22.54 RPM
SRP051959_heart	0.04 RPM	17.42 RPM
SRP051959_kidney	0.02 RPM	28.60 RPM
SRP051959_liver	0.00 RPM	25.95 RPM
SRP051959_lung	0.03 RPM	20.63 RPM
SRP051959_lymph_node	0.14 RPM	24.45 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.72 RPM
SRP051959_spleen	0.17 RPM	20.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1771 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1771 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771 , retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,