RetrogeneDB ID: retro_cjac_1058

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:94776386..94777061(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032402
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSCJAG00000016700
• Aliases: None
• Description: None

Sequence

>retro_cjac_1058
CTTAACTCTTTGAGAGCCCTTCAGCTGGAAGATGGGAGTTTCTGGGCAGTAGCCGAAGGCAGTGAAAATGACATGCGATT
TGTGTACTGTGCTTCCTGTATTTGCTATATGCTCAACTGGTCAGGCATGGATGTGAAAAAAGCCATCACCTATATTAGAA
GAAGTATGTCCTATGACAATGGCCTGGCACAGGGAGCTGGACTTGAATCTCATGGAGGATCTACTTTTTGTGGCATTGCC
TCACTCTGTCTGATGGGTAAACTAGAAGAAGTTTTTTCAGAAAAAGAATTGAACAGGATAAAGAGGTGGTGTATAATGAG
GCAGCAAAATGGTTATCATGGAAGCCCTAATAAGCTTGTAGACAGCTGTTACTCTTTTTGGGTGGAAGCAACTCTAAAGC
TTCTAAAAATTTTCCAATATACTAACTTTGAGAAAAATAGAAATTACATCTTATCATCTCAAGATTGCCTCGCAGGAGGA
TTTGCCAAGTGGCCAGACAGTCATCCAGATGCTTTGCATGCATACTTTGGGATCTGTGGCCTGTCACTAATGGAGGAAAC
TGAAATTTGTAAAGTTCATCCTGCTCTGAATGTAAGCACACGGACTTCTGAACGCCTTCTAGATCTCCATCAAAGCTGGA
AAACCAAGGACTCTAAACAATGCTCTGAGAATGTA

Alignment

ORF - retro_cjac_1058 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.92 %
• Parental protein coverage: 59.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAGLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNNWSGMDMKKAITYIRRSMSYDNGLAQGAGLE
          L..LRALQLEDGSF.AV.EGSENDMRFVYCASCICYMLN.WSGMD.KKAITYIRRSMSYDNGLAQGAGLE
Retrocopy LNSLRALQLEDGSFWAVAEGSENDMRFVYCASCICYMLN-WSGMDVKKAITYIRRSMSYDNGLAQGAGLE

Parental  SHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVGATLKLLKIFQ
          SHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHG.PNK.VD.CYSFWV.ATLKLLKIFQ
Retrocopy SHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGSPNKLVDSCYSFWVEATLKLLKIFQ

Parental  YTNFEKNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHPALNGSTRTSERLLDL
          YTNFEKNRNYILS.QD.L.GGFAKWPDSHPDALHAYFGICGLSLMEE..ICKVHPALN.STRTSERLLDL
Retrocopy YTNFEKNRNYILSSQDCLAGGFAKWPDSHPDALHAYFGICGLSLMEETEICKVHPALNVSTRTSERLLDL

Parental  HQSWKTKDSKQCSENV
          HQSWKTKDSKQCSENV
Retrocopy HQSWKTKDSKQCSENV

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	17.42 RPM
SRP051959_heart	0.02 RPM	13.73 RPM
SRP051959_kidney	0.07 RPM	21.03 RPM
SRP051959_liver	0.04 RPM	11.70 RPM
SRP051959_lung	0.02 RPM	19.23 RPM
SRP051959_lymph_node	0.05 RPM	20.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.46 RPM
SRP051959_spleen	0.04 RPM	21.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1058 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1058 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016700	1 retrocopy	retro_cjac_1058 ,
Cavia porcellus	ENSCPOG00000002443	1 retrocopy	retro_cpor_1344,
Homo sapiens	ENSG00000164219	2 retrocopies	retro_hsap_675, retro_hsap_698,
Loxodonta africana	ENSLAFG00000003752	1 retrocopy	retro_lafr_668,
Pongo abelii	ENSPPYG00000015694	3 retrocopies	retro_pabe_527, retro_pabe_545, retro_pabe_640,
Pan troglodytes	ENSPTRG00000017146	2 retrocopies	retro_ptro_444, retro_ptro_487,