RetrogeneDB ID: retro_cjac_1517

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:53855845..53856264(-)
• Located in intron of: ENSCJAG00000003921

Retrocopy information

• Ensembl ID: ENSCJAG00000004113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005632
• Aliases: None
• Description: None

Sequence

>retro_cjac_1517
GCAGAGATAGAGCGAAAGAAGAAGCGGACCTTCCGCAAGTTCACCTACCGCAGCATGGGCCTGGACCTGCTACTGGACAT
GTCCTACGAGCAGCGGATGCAGCTGAACAGTGCGCACCAGCGGTGGCTGAACCCCGGCCTGCGGCGGAAGCAGCAGTCAC
TGCTCAAGCGCCTGCGCAAGGCCGAGGCACCGCCCACGGAGAAGCCGGAAGTGGTGAAGACGCACCTGCGGGACATATTC
TGCCCAGGATGGTGGGCAGCATGGTGGGCATCTACAATGGCAAGACCTTCAACCAGGTGGAGATCAAACCAGAGATGATG
GGCCACTACCTGGGCGAGTTCTCTATCACCCACAAGCCCGGGAAGCACAGCCAGATGGGCATCAGGGCCACCCATTCCTC
CCACTTCATCCCCCTCAAG

Alignment

ORF - retro_cjac_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEVEQKKKRTFRKFTYRGVDLDQLLDMSYEHQMQLYSACQRRRQSRGLRRKQHSMLKRLRKAKKEAPPME
          AE.E.KKKRTFRKFTYR...LD.LLDMSYE..MQL.SA.Q.R....GLRRKQ.S.LKRLRKA..EAPP.E
Retrocopy AEIERKKKRTFRKFTYRSMGLDLLLDMSYEQRMQLNSAHQ-RWLNPGLRRKQQSLLKRLRKA--EAPPTE

Parental  KPEVVNTHLRDMIILP-EMVGSMVGVYNGKTFTQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSSR
          KPEVV.THLRD.I..P..MVGSMVG.YNGKTF.QVEIKPEM.GHYLGEFSIT.KP.KH...GI.ATHSS.
Retrocopy KPEVVKTHLRD-IFCP<RMVGSMVGIYNGKTFNQVEIKPEMMGHYLGEFSITHKPGKHSQMGIRATHSSH

Parental  FIPLK
          FIPLK
Retrocopy FIPLK

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	0.24 RPM	19.21 RPM
SRP051959_heart	0.21 RPM	13.72 RPM
SRP051959_kidney	0.22 RPM	14.82 RPM
SRP051959_liver	0.06 RPM	24.09 RPM
SRP051959_lung	0.36 RPM	17.21 RPM
SRP051959_lymph_node	0.05 RPM	36.07 RPM
SRP051959_skeletal_muscle	0.11 RPM	20.46 RPM
SRP051959_spleen	0.15 RPM	21.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1517 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1517 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019718	1 retrocopy	retro_btau_1856,
Callithrix jacchus	ENSCJAG00000005632	13 retrocopies	retro_cjac_143, retro_cjac_151, retro_cjac_1517 , retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Cavia porcellus	ENSCPOG00000003968	1 retrocopy	retro_cpor_495,
Dasypus novemcinctus	ENSDNOG00000000706	2 retrocopies	retro_dnov_173, retro_dnov_85,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
Felis catus	ENSFCAG00000010769	1 retrocopy	retro_fcat_1570,
Homo sapiens	ENSG00000115268	4 retrocopies	retro_hsap_1484, retro_hsap_2341, retro_hsap_2650, retro_hsap_530,
Gorilla gorilla	ENSGGOG00000002818	4 retrocopies	retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Macaca mulatta	ENSMMUG00000003050	2 retrocopies	retro_mmul_2130, retro_mmul_838,
Monodelphis domestica	ENSMODG00000005119	1 retrocopy	retro_mdom_1335,
Mus musculus	ENSMUSG00000063457	8 retrocopies	retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786, retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys	ENSNLEG00000001651	8 retrocopies	retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii	ENSOGAG00000015776	4 retrocopies	retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii	ENSPPYG00000009317	4 retrocopies	retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes	ENSPTRG00000010200	1 retrocopy	retro_ptro_122,
Pteropus vampyrus	ENSPVAG00000003168	2 retrocopies	retro_pvam_382, retro_pvam_926,
Rattus norvegicus	ENSRNOG00000024603	8 retrocopies	retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Sarcophilus harrisii	ENSSHAG00000013424	1 retrocopy	retro_shar_632,
Sus scrofa	ENSSSCG00000023248	1 retrocopy	retro_sscr_271,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,