RetrogeneDB ID: retro_ptro_2907

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:93252536..93252981(-)
• Located in intron of: ENSPTRG00000021134

Retrocopy information

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

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSPTRG00000000557
• Aliases: None
• Description: YrdC domain containing [Source:UniProtKB/TrEMBL;Acc:K7CSQ6]

Sequence

>retro_ptro_2907
TGTATGAGAGTAGTACCCCAGGAGCTCCTGAAAGACCTAGTGCCAGGACCAGTGTCCCTGGTGATGGAACGTTCAGAGGA
GCTCAACAATGACCTAAACCCCTTTACTCCTCTTACAAGGTATCCGGATTCCTGATTATGCCTTTATGCAAGACTTGGCC
AAGATGTATGAGCATCCTCTTGCTCTCACTAGTGCTGACCTCAGCTCCCAGGACAGTTCTCTGAATGCCATGGAGTTATA
AGACCTCTGGCCTCAGTTGTCCTTGGTCATTGATGGGGGACAAACTAGGGATAGCCAGATCCCTGAGTGTTACCTTGGCT
CAACTGTGGTTGACTTATCTGTGCATAGAAAGTTTGGCATCATTCGTCCAGGCTGTGTCCTGTAAAGTACTACAGCCTTC
CTTCAACAGAGGTATGGGTTGCACCCCTCATGTGCATCCTACTTG

Alignment

ORF - retro_ptro_2907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CRVRVPEGLLKDLLPGPVTLVMERSEELNKDLNPFTPLV-GIRIPDHAFMQDLAQMFEGPLALTSANLSS
          C...VP..LLKDL.PGPV.LVMERSEELN.DLNPFTPL..GIRIPD.AFMQDLA.M.E.PLALTSA.LSS
Retrocopy CMRVVPQELLKDLVPGPVSLVMERSEELNNDLNPFTPLT>GIRIPDYAFMQDLAKMYEHPLALTSADLSS

Parental  QASSLNVEEFQDLWPQLSLVIDGGQIGDGQSPECRLGSTVVDLSVPGKFGIIRPGCALESTTAILQQKYG
          Q.SSLN..E..DLWPQLSLVIDGGQ..D.Q.PEC.LGSTVVDLSV..KFGIIRPGC.L.STTA.LQQ.YG
Retrocopy QDSSLNAMEL*DLWPQLSLVIDGGQTRDSQIPECYLGSTVVDLSVHRKFGIIRPGCVL*STTAFLQQRYG

Parental  LLPSHASYL
          L.PS.ASYL
Retrocopy LHPSCASYL

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	13.53 RPM
SRP007412_cerebellum	0.00 RPM	14.55 RPM
SRP007412_heart	0.00 RPM	2.54 RPM
SRP007412_kidney	0.08 RPM	12.81 RPM
SRP007412_liver	0.00 RPM	11.82 RPM
SRP007412_testis	0.00 RPM	15.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2907 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907 , retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,