RetrogeneDB ID: retro_ptro_457

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:110475098..110475391(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf53
• Ensembl ID: ENSPTRG00000010565
• Aliases: None
• Description: chromosome 19 open reading frame 53 [Source:HGNC Symbol;Acc:24991]

Sequence

>retro_ptro_457
CTAGCGCAGGGGCAGCGCAAGTTCCAGGCGCCCAAGCCAGCTAAGAGGCAGCGGCGGCCTCTGAAAGGAACCGGGGCCGC
AGGAAAGACGGTCGTGTTACAGCTCCCAAGAAGGCGTGCGTCGGTCAGCAGCAAAAGCTTAAGAAGAATCTAGAAGTCAG
GATCTGGAAGAAGATCGAACATGCCGTGGTGATGAAAGCCAGCAACAGCCTGCCCAAGAAGCTGGCACTGCTGAAGGCCC
CGACCAAGAAGAAAGGGGCGGCTGCTGCCACCTCCTCCAACAAGACACCTTCC

Alignment

ORF - retro_ptro_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQGQRKFQAHKPAKSKT-AAAASEKNRGPRKGGRVIAPKKARVVQQQKLKKNLEVGIRKKIEHDVVMKA
          .AQGQRKFQA..P...K..AAAASE.NRG.RK.GRV.APKKA.V.QQQKLKKNLEV.I.KKIEH.VVMKA
Retrocopy LAQGQRKFQA--PKPAKR<AAAASERNRGRRKDGRVTAPKKACVGQQQKLKKNLEVRIWKKIEHAVVMKA

Parental  SSSLPKKLALLKAPAKKKGAAAATSS-KTPS
          S.SLPKKLALLKAP.KKKGAAAATSS.KTPS
Retrocopy SNSLPKKLALLKAPTKKKGAAAATSSNKTPS

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	0.02 RPM	40.36 RPM
SRP007412_cerebellum	0.04 RPM	18.68 RPM
SRP007412_heart	0.00 RPM	15.56 RPM
SRP007412_kidney	0.00 RPM	40.43 RPM
SRP007412_liver	0.00 RPM	39.90 RPM
SRP007412_testis	0.11 RPM	9.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_457 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_457 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_628
Gorilla gorilla	retro_ggor_550

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002525	1 retrocopy	retro_btau_35,
Callithrix jacchus	ENSCJAG00000004427	3 retrocopies	retro_cjac_1003, retro_cjac_2634, retro_cjac_291,
Homo sapiens	ENSG00000104979	1 retrocopy	retro_hsap_628,
Gorilla gorilla	ENSGGOG00000027024	1 retrocopy	retro_ggor_550,
Monodelphis domestica	ENSMODG00000011876	2 retrocopies	retro_mdom_1436, retro_mdom_926,
Nomascus leucogenys	ENSNLEG00000013141	1 retrocopy	retro_nleu_452,
Otolemur garnettii	ENSOGAG00000007185	1 retrocopy	retro_ogar_640,
Procavia capensis	ENSPCAG00000014250	1 retrocopy	retro_pcap_26,
Pan troglodytes	ENSPTRG00000010565	1 retrocopy	retro_ptro_457 ,
Pteropus vampyrus	ENSPVAG00000006321	1 retrocopy	retro_pvam_1140,
Tursiops truncatus	ENSTTRG00000010354	1 retrocopy	retro_ttru_317,