RetrogeneDB ID: retro_hsap_3606

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:66067006..66067270(-)
• Located in intron of: ENSG00000188107

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8orf59
• Ensembl ID: ENSG00000176731
• Aliases: None
• Description: chromosome 8 open reading frame 59 [Source:HGNC Symbol;Acc:32235]

Sequence

>retro_hsap_3606
ATGGACAAGAACAAATTAAGAGAGCAAAGGCCAGGAATGTATTTCATATAGCAAGCCAAAAAACACTTTAAGACTAAAAT
CAAAGCAACACCAGTTACCACTAATCTTCTTAAGAAGATAAACATTATGAATGATTAAGAAGTTAACAAACTGAATAAAG
CTTTTGTAAATATACAAAAAGAACTTGTACACTGCTCAGAAGGCTTTTCTGTTGAACCTCTACAGAAATGATGAGCCTCT
CAACAACATGATGAAAGTGAACCA

Alignment

ORF - retro_hsap_3606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.56 %
• Parental protein coverage: 88.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKNKLRGP-KSRNVFHIASQK-NFKAKNKAKPVTTN-LKKINIMNEEKVNRVNKAFVNVQKELAHFAKS
          M.KNKLR...K.RNVFHIASQK..FK.K.KA.PVTTN.LKKINIMN...VN..NKAFVN.QKEL.H....
Retrocopy MDKNKLREQ<KARNVFHIASQK>HFKTKIKATPVTTNLLKKINIMND*EVNKLNKAFVNIQKELVHCSEG

Parental  ISLEPLQKELIPQQRHESKP
          .S.EPLQK....QQ..ES.P
Retrocopy FSVEPLQK**ASQQHDESEP

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
bodymap2_adipose	0.00 RPM	8.95 RPM
bodymap2_adrenal	0.00 RPM	28.84 RPM
bodymap2_brain	0.00 RPM	11.09 RPM
bodymap2_breast	0.00 RPM	12.78 RPM
bodymap2_colon	0.00 RPM	15.49 RPM
bodymap2_heart	0.00 RPM	10.17 RPM
bodymap2_kidney	0.00 RPM	12.26 RPM
bodymap2_liver	0.00 RPM	12.32 RPM
bodymap2_lung	0.00 RPM	12.78 RPM
bodymap2_lymph_node	0.00 RPM	14.73 RPM
bodymap2_ovary	0.00 RPM	17.64 RPM
bodymap2_prostate	0.00 RPM	20.13 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.78 RPM
bodymap2_testis	0.00 RPM	11.69 RPM
bodymap2_thyroid	0.00 RPM	16.82 RPM
bodymap2_white_blood_cells	0.00 RPM	10.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3606 was not detected

EST

No EST(s) were mapped for retro_hsap_3606 retrocopy.

TSS

No TSS is located nearby retro_hsap_3606 retrocopy 5' end.

Lab

retro_hsap_3606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3606 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2433
Callithrix jacchus	retro_cjac_2448

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002409	2 retrocopies	retro_amel_1005, retro_amel_1049,
Bos taurus	ENSBTAG00000032227	2 retrocopies	retro_btau_158, retro_btau_7,
Callithrix jacchus	ENSCJAG00000000379	5 retrocopies	retro_cjac_1214, retro_cjac_1556, retro_cjac_1984, retro_cjac_2448, retro_cjac_2762,
Cavia porcellus	ENSCPOG00000021965	5 retrocopies	retro_cpor_201, retro_cpor_554, retro_cpor_765, retro_cpor_841, retro_cpor_962,
Felis catus	ENSFCAG00000026366	1 retrocopy	retro_fcat_450,
Homo sapiens	ENSG00000176731	4 retrocopies	retro_hsap_2609, retro_hsap_3163, retro_hsap_3606 , retro_hsap_52,
Gorilla gorilla	ENSGGOG00000027464	4 retrocopies	retro_ggor_1218, retro_ggor_1353, retro_ggor_1828, retro_ggor_2433,
Loxodonta africana	ENSLAFG00000032612	4 retrocopies	retro_lafr_1083, retro_lafr_1242, retro_lafr_911, retro_lafr_944,
Myotis lucifugus	ENSMLUG00000006155	1 retrocopy	retro_mluc_1272,
Macaca mulatta	ENSMMUG00000006381	3 retrocopies	retro_mmul_1475, retro_mmul_2490, retro_mmul_537,
Mus musculus	ENSMUSG00000078784	3 retrocopies	retro_mmus_257, retro_mmus_2950, retro_mmus_3313,
Pongo abelii	ENSPPYG00000029910	3 retrocopies	retro_pabe_2345, retro_pabe_2630, retro_pabe_3633,
Pan troglodytes	ENSPTRG00000020385	5 retrocopies	retro_ptro_1759, retro_ptro_2275, retro_ptro_2437, retro_ptro_2982, retro_ptro_471,
Rattus norvegicus	ENSRNOG00000038902	2 retrocopies	retro_rnor_2600, retro_rnor_496,
Sus scrofa	ENSSSCG00000006144	2 retrocopies	retro_sscr_342, retro_sscr_96,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).