RetrogeneDB ID: retro_cjac_3006

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:93870392..93871253(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000016017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSCJAG00000000624
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_cjac_3006
TGCACGTGTCCCACCAACAAGATGACCGTGTGCAGCCCCGACGGCCCCGGCGGCCGCTGCCAGTGCCGTGCGCTGGGCTC
GGGCGTGGCGGTCGACTGCTCCACGCTGACCTCCAAGTGTCTGCTCCTGAAGGCGCGCATGAGCGCCCCCAAGAGCGCGC
GCACGCTGGTGCGGCCGAGCGAACACGCGTTCGTGGACAACGACGGCCTCTACGACCCCGACTGCGACCCCGAGGGCCGC
TTCAAGGCGCGCCAGTGCAACCAGACGTCGGTGTGCTGGTGCGTGAACTCGGTGGGCGTGCGCCGCACCGACAAGGGCGA
CCTGAGCCTGCGCTGCGAGGAGCTGGTGCGCACTCATCATATCCTCATCGACCTGCGCCACCGCCCCACCGCCGGCGCCT
TCAACCACTCTGACCTGGACGCCGAGCTGCGGCGGCTCTTCCGCGAGCGCTATCGGCTGCACCCCAAGTTCGTGGCGGCC
GTGCACTATAAGCAGCCCACCATCCAGATCGAGCTGCAGCAGAACACGTCGCAGAAAATCGCCGGCGACGTGGACATCGG
CGATGCCGCCTACTACTTCGAGAGGGACATCAAGGGCGAATCTCTGTTCCAGAGCCGCGGCGGCCTGGACTTGCGCGTGC
GCGGCGAGCCCCTGCAGGTGGAGCGCACGCTTATCTACTACCTGGACGAGAAGCCCCCGAAGTTTTCAATGAAGCGCCTC
ACCGCCGGCCTCATCGCGGTCATCGTGGTGGTCGTGGTGGCCCTCGTCGCCGGCGTGGTCGTCCTGGTGATCACCAACCG
GAGAAAGTCGGGGAAGTACAAGAAGGTGGAGATCAAGGAACTGGGGGAGTTGAGAAAGGAA

Alignment

ORF - retro_cjac_3006 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.87 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CHCENYKLAINCVMNSNGQCQCTSVGSQNTVICSKLASKCLVMKAEITNSKLGRR-AKP-EGALQNNDGL
          C.C...K..........G.CQC...GS...V.CS.L.SKCL..KA.....K..R....P.E.A...NDGL
Retrocopy CTCPTNKMTVCSPDGPGGRCQCRALGSGVAVDCSTLTSKCLLLKARMSAPKSARTLVRPSEHAFVDNDGL

Parental  YDPDCDESGLFKAKQCNGTSTCWCVNTAGVRRTDK-DTEITCSERVRTFWIIIELKHKAREKPYDVQSLR
          YDPDCD..G.FKA.QCN.TS.CWCVN..GVRRTDK.D....C.E.VRT..I.I.L.H...........L.
Retrocopy YDPDCDPEGRFKARQCNQTSVCWCVNSVGVRRTDKGDLSLRCEELVRTHHILIDLRHRPTAGAFNHSDLD

Parental  DALQEAITTRYHLDGKFITNVVYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHPSKKMD
          ..L......RY.L..KF...V.Y....I.I.L.QN.SQK...DVDI.D.AYYFE.D.KGESLF......D
Retrocopy AELRRLFRERYRLHPKFVAAVHYKQPTIQIELQQNTSQKIAGDVDIGDAAYYFERDIKGESLFQSRGGLD

Parental  LRVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKAGVIAVIVVVVIAIVAGIVVLVVSRKKRMAKYQKAEI
          LRV.GE.L......TLIYY.DEK.P.FSM..L.AG.IAVIVVVV.A.VAG.VVLV........KY.K.EI
Retrocopy LRVRGEPLQVE--RTLIYYLDEKPPKFSMKRLTAGLIAVIVVVVVALVAGVVVLVITNRRKSGKYKKVEI

Parental  KEMGEMNRE
          KE.GE...E
Retrocopy KELGELRKE

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	0.38 RPM	523.14 RPM
SRP051959_heart	0.05 RPM	0.02 RPM
SRP051959_kidney	6.52 RPM	53.65 RPM
SRP051959_liver	0.13 RPM	2.27 RPM
SRP051959_lung	4.42 RPM	21.94 RPM
SRP051959_lymph_node	0.14 RPM	0.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.61 RPM	0.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3006 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3006 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_92
Macaca mulatta	retro_mmul_34
Bos taurus	retro_btau_66
Sus scrofa	retro_sscr_69

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006 ,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,