RetrogeneDB ID: retro_ptro_998

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:30486428..30487250(+)
• Located in intron of: ENSPTRG00000006872

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1QBP
• Ensembl ID: ENSPTRG00000008631
• Aliases: C1QBP, gC1qR
• Description: None

Sequence

>retro_ptro_998
CCTCTGTGATGCTGCATGCCTGGTGCCCCGGGCTCCGCAGTTGCTGCCCTCCATGCTACCATGCCTGCCCCACCACTCCA
GCAGCGCCCAGGTCCTGTGCCCGGCCCTTTGCGCTGCTCAGTGTGCATGTGTGTGGGGTCTGCATGGCAGCCTGGCCTCC
TGGGGCCTCCTAGGCCCTCCTAGGCCCTGTGCATGGGGCTACAGCGGCTGTGCGCTGCACACCAAAGGAGACAAAGCTTC
TGTTGAGTTCCTGAGTGATGAAATTAAGGAGGAAAGGGAAATCGAGAAGCATAAGAGGCATTCCCTCCCTAAGAGGTCTG
GAAGTTGGGAGCTAGAATTTAAATGGAACAGAAGCTAAATTAGCATGGCAAGTTGCCAGGGGAAAGATCTCTGTCACTTT
CAACATTATCAACAGCATCCCACGCAAGTCTGATGGTGAGGAGGAGCCCTCACAAGGGCTGTAGGTTGCAGAATAGGATT
CTGAATTGACATCAACTCCCAATTTCATAGTTGAAGTTATGAAGAATGATAGCAAGAAGGTCCTGGTGCTGTCACTATCA
GAGGATGAGTTTGGACAAGAGCAGGTGGAGAGTAACATTTTCTCCATCAAGGATGTTAGCTTTCAGTCCAATGGCAAGTC
TGGATGTTAGGGCACTAGTACACACTCAACACAGAGTCCCCGGACTAGGCCCTGTATTATTTCTTTGAGGACAAAGGGGT
GGAAACGCTTTTGTGGATGGGTTGGTGGAGCTCAGCACAGTTCCGGAGCACCAGGAGGACATTACTTTTCTTGAAAATCT
CAAAAGTTTTGTCAAGGACCAG

Alignment

ORF - retro_ptro_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PLLRCVPRVLGSSVAGLRAAAPASPFRQLLQPAP-RLCTRPFGLLSVRAGSERRPGLLRPRGPCACGCGC
          PL..C.P...GS.VA.L.A..PA.P..Q...P.P..LC...........GS....GLL.P..PCA.G...
Retrocopy PL*CCMPGAPGSAVAALHATMPAPPLQQRPGPVP>ALCAAQCACVWGLHGSLASWGLLGPPRPCAWGYSG

Parental  GSLHTDGDKAFVDFLSDEIKEERKIQKHK--SLPKMSGGWELE-LNGTEAKLVRKVAGEKITVTFNINNS
          ..LHT.GDKA.V.FLSDEIKEER.I.KHK..SLPK.SG.WELE.LNGTEAKL...VA..KI.VTFNI.NS
Retrocopy CALHTKGDKASVEFLSDEIKEEREIEKHKRHSLPKRSGSWELE>LNGTEAKLAWQVARGKISVTFNIINS

Parental  IPPTFDGEEEPSQGQKVEEQEPELTSTPNFVVEVIKNDDGKKALVLDCHYPEDEVGQEDEAESDIFSIRE
          IP...DGEEEPSQG..V.E...ELTSTPNF.VEV.KN.D.KK.LVL.....EDE.GQE...ES.IFSI..
Retrocopy IPRKSDGEEEPSQGL*VAE*DSELTSTPNFIVEVMKN-DSKKVLVLS--LSEDEFGQE-QVESNIFSIKD

Parental  VSFQSTGESEWKDTN-YTLNTDSLDWALYDHLMDFLADRGVD-NTFADELVELSTALEHQEYITFLEDLK
          VSFQS.G.S....T..YTLNT.S.D.ALY....D.....GV..N.F.D.LVELST..EHQE.ITFLE.LK
Retrocopy VSFQSNGKSGC*GTS<YTLNTESPD*ALYYFFED----KGVE<NAFVDGLVELSTVPEHQEDITFLENLK

Parental  SFVKSQ
          SFVK.Q
Retrocopy SFVKDQ

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	0.04 RPM	28.56 RPM
SRP007412_cerebellum	0.00 RPM	43.02 RPM
SRP007412_heart	0.00 RPM	39.52 RPM
SRP007412_kidney	0.00 RPM	55.21 RPM
SRP007412_liver	0.00 RPM	46.55 RPM
SRP007412_testis	0.00 RPM	20.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_998 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_998 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1475
Gorilla gorilla	retro_ggor_1133
Pongo abelii	retro_pabe_1222
Callithrix jacchus	retro_cjac_680

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006043	2 retrocopies	retro_amel_1734, retro_amel_356,
Callithrix jacchus	ENSCJAG00000011352	6 retrocopies	retro_cjac_2041, retro_cjac_2408, retro_cjac_4033, retro_cjac_604, retro_cjac_680, retro_cjac_946,
Dasypus novemcinctus	ENSDNOG00000008887	3 retrocopies	retro_dnov_1151, retro_dnov_1946, retro_dnov_702,
Felis catus	ENSFCAG00000026474	3 retrocopies	retro_fcat_1135, retro_fcat_1763, retro_fcat_892,
Homo sapiens	ENSG00000108561	2 retrocopies	retro_hsap_1475, retro_hsap_2516,
Gorilla gorilla	ENSGGOG00000002745	5 retrocopies	retro_ggor_1133, retro_ggor_1569, retro_ggor_3007, retro_ggor_3008, retro_ggor_717,
Macropus eugenii	ENSMEUG00000014882	13 retrocopies	retro_meug_1068, retro_meug_1347, retro_meug_1363, retro_meug_1446, retro_meug_1901, retro_meug_1940, retro_meug_1970, retro_meug_2069, retro_meug_2128, retro_meug_434, retro_meug_580, retro_meug_988, retro_meug_989,
Macaca mulatta	ENSMMUG00000006592	1 retrocopy	retro_mmul_1554,
Nomascus leucogenys	ENSNLEG00000009081	2 retrocopies	retro_nleu_2379, retro_nleu_3038,
Otolemur garnettii	ENSOGAG00000001610	5 retrocopies	retro_ogar_1376, retro_ogar_2502, retro_ogar_2518, retro_ogar_2879, retro_ogar_768,
Ochotona princeps	ENSOPRG00000013150	1 retrocopy	retro_opri_408,
Pongo abelii	ENSPPYG00000007870	6 retrocopies	retro_pabe_1222, retro_pabe_1385, retro_pabe_1413, retro_pabe_1866, retro_pabe_1868, retro_pabe_670,
Pan troglodytes	ENSPTRG00000008631	3 retrocopies	retro_ptro_1140, retro_ptro_1461, retro_ptro_998 ,
Pteropus vampyrus	ENSPVAG00000002466	1 retrocopy	retro_pvam_384,
Sarcophilus harrisii	ENSSHAG00000002441	2 retrocopies	retro_shar_620, retro_shar_813,