RetrogeneDB ID: retro_cjac_4157

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:45602632..45603007(-)
• Located in intron of: ENSCJAG00000012004

Retrocopy information

• Ensembl ID: ENSCJAG00000012024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP1A
• Ensembl ID: ENSCJAG00000020908
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:F6SFB9]

Sequence

>retro_cjac_4157
CGGTCCACGCTGCCCATCCCGCTGCCTGCCTACCCAGCATCTGCCACCGCCATGGGAGTGCAGGTGGAAACCATCTCCCC
AGGAGACGGGTGCACCTTCCCGAAGTGCAGCCAGACCTGCGTGGTGCACTATACCCGGATGCTTGAAGATGGAAAGAAAT
TTGATTCCTCCTGGGACACAAACAAGCCCTTTAAGTTTATGCTAGGCAAGCAGGAGGTGATGAGAGGCTGGGAAGAAGGA
GTTGCGCAGATGAGTGTGGGTCAGAGAGCCAAACTGACTGTATCTCCAGATTATGCCTATGGTGCCACTGGGCACCCAGG
CATCATCCCACCATGTGCCACTCTCATCTTCGATGTGGAGCTTCTAAAACTGGAG

Alignment

ORF - retro_cjac_4157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.0 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSTPPVALPARPASAAAMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGK
          RST.P..LPA.PASA.AMGVQVETISPGDG.TFPK..QTCVVHYT.MLEDGKKFDSS.D.NKPFKFMLGK
Retrocopy RSTLPIPLPAYPASATAMGVQVETISPGDGCTFPKCSQTCVVHYTRMLEDGKKFDSSWDTNKPFKFMLGK

Parental  QEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
          QEV.RGWEEGVAQMSVGQRAKLT.SPDYAYGATGHPGIIPP.ATL.FDVELLKLE
Retrocopy QEVMRGWEEGVAQMSVGQRAKLTVSPDYAYGATGHPGIIPPCATLIFDVELLKLE

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	0.02 RPM	10.89 RPM
SRP051959_heart	0.02 RPM	9.31 RPM
SRP051959_kidney	0.04 RPM	8.19 RPM
SRP051959_liver	0.00 RPM	7.45 RPM
SRP051959_lung	0.11 RPM	11.13 RPM
SRP051959_lymph_node	0.11 RPM	6.87 RPM
SRP051959_skeletal_muscle	0.02 RPM	8.98 RPM
SRP051959_spleen	0.04 RPM	8.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4157 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4157 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157 , retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,