RetrogeneDB ID: retro_cjac_680

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:42918735..42919415(+)
• Located in intron of: ENSCJAG00000035611

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1QBP
• Ensembl ID: ENSCJAG00000011352
• Aliases: None
• Description: complement component 1, q subcomponent binding protein [Source:HGNC Symbol;Acc:1243]

Sequence

>retro_cjac_680
GGGTCTGCACGGCAGCTTGGCCTCCTGTAGCCTCCTAGGCCCTGTGCCCGTGACTACAGCAGCTGCGCACTGCACACCAA
AGGAAACAAAGCTTCTATTGAATTTCTGAGTGATGAAATTAAGGAGGAAAGAAAAATCCAGAAGCCTAAGAGACATTCCC
TCCCTAGGAGGTCTGGAAGGTGGGAGCTAGAATTTAAATGGAACCGAAGCTAAATTAGTGTGGCAAGTTGCCAGGGGAAA
GATCACTGTCGCTTTCACTATTAACAACAGCACCCCACCCACATCTGATGGTGAGGAGGAGCCTTCACAAGGGCAGAACA
TTGAAGAATGGGATTCTGAATTGACATCAACTCCCAATTTCATAGTTATGAAGAATGGTGGCAAGAAGGCCCTGGTACTG
AATCATCGCCATCAGAGGATGAGTTGGGACAAGAAGAGCAGGTGGAGAGTAACATTTTCTCCATCAGGAAGGTTAGCTGT
CAGTCCAATGGCAAGTCTGGATGGAAAGACACTAGTACACACTCAACACAAAGTCCCCAGACTAGGCTTTGTATTATTTC
CTGGAGGACCAAGGGGTGAACGTCGCTTTTGTGCATGGGTTGATGGCGCTCAGCACAGTTTTGCAGCACCAGGAGGACGT
TACTTTTCTTGAAGATCTCAAAAGTTTTGCAAAGAGCCAG

Alignment

ORF - retro_cjac_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.29 %
• Parental protein coverage: 81.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSEQRPGLLRPRGPCACGCGCGALHTEGDKAFVDFLSDEIKEERKIQKHK--TLPKMSGGWELE-LNGTE
          GS....GLL.P..PCA......ALHT.G.KA...FLSDEIKEERKIQK.K...LP..SG.WELE.LNGTE
Retrocopy GSARQLGLL*PPRPCARDYSSCALHTKGNKASIEFLSDEIKEERKIQKPKRHSLPRRSGRWELE>LNGTE

Parental  AKLVQKVAGETITVTFNINNSIPPTFDGEEEPSKGQKVEEQEPELTSTPNFVVEVIKNDGKKALVLDCHY
          AKLV..VA...ITV.F.INNS.PPT.DGEEEPS.GQ..EE...ELTSTPNF...V.KN.GKKALVL....
Retrocopy AKLVWQVARGKITVAFTINNSTPPTSDGEEEPSQGQNIEEWDSELTSTPNFI--VMKNGGKKALVLNHRH

Parental  -PEDEVGQEDEAESDIFSIREVSFQSTGNSEWKDTN-YTLNTDSLDWALYDHLMDFLADRGVDNTFADEL
          ..EDE.GQE...ES.IFSIR.VS.QS.G.S.WKDT..YTLNT.S.D.ALY..L.D.....GV...F...L
Retrocopy <SEDELGQEEQVESNIFSIRKVSCQSNGKSGWKDTS<YTLNTKSPD*ALYYFLED----QGVNVAFVHGL

Parental  VELSTALEHQEYITFLEDLKSFVKSK
          ..LST.L.HQE..TFLEDLKSF.KS.
Retrocopy MALSTVLQHQEDVTFLEDLKSFAKSQ

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
SRP051959_colon	0.00 RPM	16.73 RPM
SRP051959_heart	0.04 RPM	14.91 RPM
SRP051959_kidney	0.00 RPM	16.88 RPM
SRP051959_liver	0.00 RPM	26.40 RPM
SRP051959_lung	0.00 RPM	9.87 RPM
SRP051959_lymph_node	0.00 RPM	14.98 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.32 RPM
SRP051959_spleen	0.00 RPM	13.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_680 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_680 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1475
Pan troglodytes	retro_ptro_998
Gorilla gorilla	retro_ggor_1133
Pongo abelii	retro_pabe_1222

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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,