RetrogeneDB ID: retro_cjac_1495

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:4493636..4494221(-)
• Located in intron of: ENSCJAG00000014675

Retrocopy information

• Ensembl ID: ENSCJAG00000014693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001993
• Aliases: None
• Description: None

Sequence

>retro_cjac_1495
CAGAAGAAGAGAACTCTCATGATGGAAATATTTTTTTAACTAAAGATGTATTTCAACTAAAAGACTTGGAGAAGATTTCT
CCCGAAGAGAGAGGCATCACTTCTTCGTCAGTCAAAGAAGTCCTTCAAAGCTTAGTTGATGATGGGATGGTTGACTGTGA
GATGATTGGAACTTCTAATTATTACTGGGCTTTTCCAAGTAAAGCTCTTCATGCAAGGAAACTTAAGTTGGAGTCCCTGG
AATCTCAGTTGTCTGAGGGAAGCCAAAAGCAGGCAAGCCTAAAGGAAAGCATTGAAAAGGCTAAAATTGGCCGATGTGAA
ATGGAAGAGCGAACAACGCCAGCAAAAGAACTTTCTTCACTTTGAGACCAAAGGGCAAGCTAAAGGCAGAAGTCGAAAAA
TACAAAAATTGTGACCCACAAGTCGTGGAAGAAATATGTCAAGAAAGTAAAGGAGCCAAAGATGCTGCTAACATATGGAC
TCATAACATATTTGCAATAGAATCTTGGGCAAAAAGAAAATTTGGGTTCGAAGAAAATAAAATTGATAAAACTCTTGGAA
TTCCAGAAGACTTGACTACATAGAC

Alignment

ORF - retro_cjac_1495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.41 %
• Parental protein coverage: 95.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEKRTRMMEIFF-ETKDVFQLKDLEKIAPKEKGITSMSVKEVLQSLVDDSMVDCERIGTSNYYWAFPSKA
          ..KRT.MMEIFF..TKDVFQLKDLEKI.P.E.GITS.SVKEVLQSLVDD.MVDCE.IGTSNYYWAFPSKA
Retrocopy QKKRTLMMEIFF<LTKDVFQLKDLEKISPEERGITSSSVKEVLQSLVDDGMVDCEMIGTSNYYWAFPSKA

Parental  LHARKRKLEALESQLSEGSQKHASLQKSIEKAKIGRCETEERTMLAKELSSLRDQRE-QLKAEVEKYKDC
          LHARK.KLE.LESQLSEGSQK.ASL..SIEKAKIGRCE.EERT..AKELSSL.DQR...LKAEVEKYK.C
Retrocopy LHARKLKLESLESQLSEGSQKQASLKESIEKAKIGRCEMEERTTPAKELSSL*DQRA<KLKAEVEKYKNC

Parental  DPQVVEEIRQVNKVAKEAANRWTDNIFAIKSWAKRKFGFEENKIDKTFGIPED-FDYID
          DPQVVEEI.Q..K.AK.AAN.WT.NIFAI.SWAKRKFGFEENKIDKT.GIPED..DYID
Retrocopy DPQVVEEICQESKGAKDAANIWTHNIFAIESWAKRKFGFEENKIDKTLGIPED<LDYID

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	1.38 RPM
SRP051959_heart	0.14 RPM	0.11 RPM
SRP051959_kidney	0.00 RPM	0.09 RPM
SRP051959_liver	0.00 RPM	0.06 RPM
SRP051959_lung	0.07 RPM	0.31 RPM
SRP051959_lymph_node	0.00 RPM	1.19 RPM
SRP051959_skeletal_muscle	0.24 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1495 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495 , retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,