RetrogeneDB ID: retro_ptro_824

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:51766150..51767659(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UTP14A
• Ensembl ID: ENSPTRG00000022262
• Aliases: None
• Description: UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) [Source:HGNC Symbol;Acc:10665]

Sequence

>retro_ptro_824
GCCTTAAAAGAGTTTGAGCAGCTACAGAAGGTTAATCCAACTGTGGCATTGGAAGAAATGGAAAAAATTGAAAATGCCAG
AATGATGGAAAGAATGAGCCTTAAGCACCAAAACAGTGGGAAATGGGCCAAGTCAAAGGCAATTATGGCCAAATATGACC
TGGAGGCTCGCCAAGCTATGCAGGAACAGTTGGCCAAGAACAAAGAACTGACACAGAAACTCCAGGTAGCCTCTGAGAGT
GAGGAAGAGGAGGGAGGCACAGAAGTGGAAGAACTCCTTGTCCCTCATGTAGTGAATGAAGTGCAGATGAATGTGGACGG
ACCGAATCCCTGGATGTTCAGGAGCTGCACCAGTGACACCAAAGAGGCTGCAACACAGGAGGACCCTGAGCAACTGCCAG
AGCTTGCAGCTCATGAGGTTTCTGCAAGTGGGGCAGAAGAAAGACCAGTGGCAGAGGAAGAAATTTTGTTGAGAGAATTT
GAGGAGAGGCAATCCCTTAGAAAAAGATCTGAGCTCAACCAGGATGCTGAGCCAGCAAGCAGTCAAGAAACAAAAGATTC
TAGCAGCCAGGAGGTGCTGTCCGAATTGAGGGCACTATCTCAGAAATTGAAGGAAAAACATCAGTCCAGGAAGCAAAAAG
CAAGTTCAGAGGGGACTGTTCCCCAGGTCCAGAGAGAGGAACCTGCCCCAGAAGAAGCGGAACCCCTATTGCTACAGAGG
TCAGAAAGAGTACAAACTCTGGAAGAGCTAGAAGAGCTGGGAAAAGAAGATTGTTTTCAAAATAAGGAGCTTCCCAGACC
TTTGTTAGAAGGACAGCAGTCAGAGAGGACCCCAAATAATCGGCCTGATGCCCCTAAGGAGAAGAAAGAGAAGGAGCAAC
TGATCAACCTACAGAACTTCCTAACCACACAGTCTCCTTCCGTGAGGTCTTTGGCAGTTCCCACAATAATAGAGGAGCTG
GAAGATGAAGAGGAGAGAGACCAAAGGCAGATGATAAAGGAAGCTTTTGCTGGGGATGATGTCATCAGAGATTTCTTGAA
AGAGAAGAGGGAAGCTGTGGAGGCAAGTAAGCCAAAGGACGTGGACCTGACACTACCTGGCTGGGGCGAGTGGGGTGGTG
TGGGCCTAAAGCCCAGTGCCAAGAAAAGACGCCAGTTTCTCATTAAAGCCCCTGAGGGTCCTCCAAGAAAAGATAAGAAT
TTGCCAAATGTGATTATCAGTGAGAAGCGCAACATCCACGCAGCAGCTCATCAGGTACAAGTGCTTCCATATCCATTTAC
CCACCATCGGCAATTTGAAAGGACCATCCAGACCCCTATAGGATCCACATGGAACACCCAGAGGGCTTTCCAAAAGCTGA
CTACTCCCAAGGTCGTCACCAAGCCAGGCCATATCATTAAGCCCATAAAAGCAGAGGATGTGGGCTACCAGTCTTCCTCA
AGGTCAGACCTGCCTGTCATACAGAGGAATCCAAAACGAATCACCACACGTCACAATAAAGAAGAAAAA

Alignment

ORF - retro_ptro_824 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.67 %
• Parental protein coverage: 73.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALKEFEQLRKVNPAAALEELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLSKNKEL
          ALKEFEQL.KVNP..ALEE.EKIE.ARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQL.KNKEL
Retrocopy ALKEFEQLQKVNPTVALEEMEKIENARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKEL

Parental  TQKLQVASESEEEEGGTEDVEELLVPDVVNEVQMNADGPNPWMLRSCTSDTKEAATQEDPEQLPELEAHG
          TQKLQVASESEEEEGGTE.VEELLVP.VVNEVQMN.DGPNPWM.RSCTSDTKEAATQEDPEQLPEL.AH.
Retrocopy TQKLQVASESEEEEGGTE-VEELLVPHVVNEVQMNVDGPNPWMFRSCTSDTKEAATQEDPEQLPELAAHE

Parental  VSESEGEERPMAEEEILLREFEERRSLRKRSELSQDAEPAGSQETIDSGSQEVLSELRVLSQKLKENHQS
          VS.S..EERP.AEEEILLREFEER.SLRKRSEL.QDAEPA.SQET.DS.SQEVLSELR.LSQKLKE.HQS
Retrocopy VSASGAEERPVAEEEILLREFEERQSLRKRSELNQDAEPASSQETKDSSSQEVLSELRALSQKLKEKHQS

Parental  RKQKASSEGTIPQVQREEPAPEEEEPLLLQRPERVQTLEELEELGKEECFQNKELPRPVLEEQQSERTPN
          RKQKASSEGT.PQVQREEPAPEE.EPLLLQR.ERVQTLEELEELGKE.CFQNKELPRP.LE.QQSERTPN
Retrocopy RKQKASSEGTVPQVQREEPAPEEAEPLLLQRSERVQTLEELEELGKEDCFQNKELPRPLLEGQQSERTPN

Parental  NRPDAPKEKKKKEQMIDLQNLLTTQSPSVKSLAVPT-IEELEDEEERNHRQMIKEAFAGDDVIRDFLKEK
          NRPDAPKEKK.KEQ.I.LQN.LTTQSPSV.SLAVPT.IEELEDEEER..RQMIKEAFAGDDVIRDFLKEK
Retrocopy NRPDAPKEKKEKEQLINLQNFLTTQSPSVRSLAVPTIIEELEDEEERDQRQMIKEAFAGDDVIRDFLKEK

Parental  REAVEASKPKDVDLTLPGWGEWGGVGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNIHAAAHQV
          REAVEASKPKDVDLTLPGWGEWGGVGLKPSAKKRR.FLIKAPEGPPRKDKNLPNVII.EKRNIHAAAHQV
Retrocopy REAVEASKPKDVDLTLPGWGEWGGVGLKPSAKKRRQFLIKAPEGPPRKDKNLPNVIISEKRNIHAAAHQV

Parental  QVLPFPFTHHWQFERTIQTPIGSTWNTQRAFQKLTTPKVVTKPGHIINPIKAEDVGYRSSSRSDLSVIQR
          QVLP.PFTHH.QFERTIQTPIGSTWNTQRAFQKLTTPKVVTKPGHII.PIKAEDVGY.SSSRSDL.VIQR
Retrocopy QVLPYPFTHHRQFERTIQTPIGSTWNTQRAFQKLTTPKVVTKPGHIIKPIKAEDVGYQSSSRSDLPVIQR

Parental  NPKRITTRHKKQLK
          NPKRITTRH.K..K
Retrocopy NPKRITTRHNKEEK

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	5.88 RPM	7.61 RPM
SRP007412_cerebellum	12.91 RPM	9.32 RPM
SRP007412_heart	8.34 RPM	4.28 RPM
SRP007412_kidney	14.78 RPM	6.62 RPM
SRP007412_liver	8.18 RPM	7.46 RPM
SRP007412_testis	9.17 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_824 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_824 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_29
Gorilla gorilla	retro_ggor_163

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824 ,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,