RetrogeneDB ID: retro_ptro_92

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:59106888..59107863(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000000795
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSPTRG00000011902
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_ptro_92
ATGGCTCGGGGCCCCGGCCTCGCGCCGCCACCGCTGCGGCTGCCGCTGCTGCTGCTGCTGGTGCTGGCGGCGGTGACCGG
CCACACGGCCGCGCAGGACAACTGCACGTGTCCCACCAACAAGATGACCGTGTGCAGCCCCGACGGCCCCGGCGGCCGCT
GCCAGTGCCGCGCGCTGGGCTCGGGCATGGCGGTCGACTGCTCCACGCTGACCTCCAAGTGTCTGCTGCTCAAGGCGCGC
ATGAGCGCCCCCAAGAACGCCCGCACGCTGGTGCGGCCGAGTGAGCACGCGCTCGTGGACAACGATGGCCTCTACGACCC
CGACTGCGACCCCGAGGGCCGCTTCAAGGCGCGCCAGTGCAACCAGACGTCGGTGTGCTGGTGCGTGAACTCGGTGGGCG
TGCGCCGCACGGACAAGGGCGACCTGAGCCTACGCTGCGATGAGCTGGTGCGCACCCACCACATCCTCATTGACCTGCGC
CACCGCCCCACCGCCGGCGCCTTCAACCACTCAGACCTGGACGCCGAGCTGAGGCGGCTCTTCCGCGAGCGCTATCGGCT
GCACCCCAAGTTCGTGGCGGCCGTGCACTACGAGCAGCCCACCATCCAGATCGAGCTGCGGCAGAACACGTCGCAGAAGG
CCGCCGGTGACGTGGATATCGGCGATGCCGCCTACTACTTCGAGAGGGACATCAAGGGCGAGTCTCTATTCCAGGGCCGC
GGCGGCCTGGACTTGCGCGTGCGCGGAGAACCCCTGCAGGTGGAGCGCACGCTCATCTATTACCTGGACGAGATCCCCCC
GAAGTTCTCCATGAAGCGCCTCACCGCCGGCCTCATCGCCGTCATCGTGGTGGTCGTGGTGGCCCTCGTCGCCGGCATGG
CCGTCCTGGTGATCACCAACCGGAGAAAGTCGGGGAAGTACAAGAAGGTGGAGATCAAGGAACTGGGGGAGTTGAGAAAG
GAACCGAGCTTGTAG

Alignment

ORF - retro_ptro_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.17 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVCENYKLAVNCFVNNNHQCQCTSIGAQNTVICSKLAAKCLVMKAEMNGSKLGRR-AKP-EGALQNNDGL
          C.C...K..V.........CQC...G....V.CS.L..KCL..KA.M...K..R....P.E.AL..NDGL
Retrocopy CTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGL

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

Parental  TALQKEITTRYQLDPKFITNILYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHSK-KMD
          ..L......RY.L.PKF.....YE...I.I.L.QN.SQK...DVDI.D.AYYFE.D.KGESLF......D
Retrocopy AELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQNTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLD

Parental  LTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKAGVIAVIVVVVIAVVAGIVVLVFSRKKRMAKYEKAEI
          L.V.GE.L......TLIYY.DE..P.FSM..L.AG.IAVIVVVV.A.VAG..VLV........KY.K.EI
Retrocopy LRVRGEPLQVE--RTLIYYLDEIPPKFSMKRLTAGLIAVIVVVVVALVAGMAVLVITNRRKSGKYKKVEI

Parental  KEMGEMHRE
          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
SRP007412_brain_prefrontal_cortex	0.21 RPM	1.14 RPM
SRP007412_cerebellum	0.00 RPM	0.22 RPM
SRP007412_heart	0.00 RPM	0.26 RPM
SRP007412_kidney	20.95 RPM	181.89 RPM
SRP007412_liver	0.75 RPM	8.94 RPM
SRP007412_testis	0.11 RPM	11.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_92 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_92 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_92 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_34
Callithrix jacchus	retro_cjac_3006
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,