RetrogeneDB ID: retro_hsap_1799

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:5415362..5415857(-)
• Located in intron of: ENSG00000091592

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSG00000131732
• Aliases: ZCCHC9, PPP1R41
• Description: zinc finger, CCHC domain containing 9 [Source:HGNC Symbol;Acc:25424]

Sequence

>retro_hsap_1799
CTCCAAGAGGACAGTCAATGGGAAGTAAGAAGATTTAAAAGACAAGGGGCAAAGAAAAATGCAATGGTGTGTTTCCATTG
TAGAAAACCTGGTCGTGGAATTGCGGATTGCCCTGCCGCCCTTGAAAATCAAGATATGGGCACTAGAAGATGTTACAAGT
GTGGGTCCACAGATCACGAAATAACCAAGTGTAAGGCTAAAGTAGACCCGCCTCTTGGCGAATGTCCTTTTGCAGAATGT
TTTGTCTGTGGAGAAATGGGGCACCTGTCTAGATCTTGTCCTGATAATCCCAAAGGACTCTATGCTGATGGTAGTGGTTG
CCAACTTCATGGCTCTGTGGAACATTTAAAGAAAGATTGCCCTGAAAGTGAGAATTCAGATCGAATGGCCACAGTTGGTC
TGTGGGCAAAGGGAATAAGTGCAGACTATGAAGACATTGTGGATGCACCAAAACCACAAAAACCCAAAACAAAAATACCT
AAAGGTGTTAATTTT

Alignment

ORF - retro_hsap_1799 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 60.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHGIADCPAALENQDMGTGICYRCGSTEHEITKCKAKVDP
          L..DS..E.RR.KRQ.AKKNAMVCFHCRKPG.GIADCPAALENQDMGT..CY.CGST.HEITKCKAKVDP
Retrocopy LQEDSQWEVRRFKRQGAKKNAMVCFHCRKPGRGIADCPAALENQDMGTRRCYKCGSTDHEITKCKAKVDP

Parental  ALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYADGGGCKLCGSVEHLKKDCPESQNSERMVTVGRWAKGMS
          .LGE.PFA.CFVCGEMGHLSRSCPDNPKGLYADG.GC.L.GSVEHLKKDCPES.NS.RM.TVG.WAKG.S
Retrocopy PLGECPFAECFVCGEMGHLSRSCPDNPKGLYADGSGCQLHGSVEHLKKDCPESENSDRMATVGLWAKGIS

Parental  ADYEEILDVPKPQKPKTKIPKVVNF
          ADYE.I.D...........PK.VNF
Retrocopy ADYEDIVDAXXXXXXXXXXPKGVNF

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	0.10 RPM	9.84 RPM
bodymap2_adrenal	0.70 RPM	17.17 RPM
bodymap2_brain	0.00 RPM	8.60 RPM
bodymap2_breast	0.82 RPM	17.53 RPM
bodymap2_colon	0.15 RPM	17.77 RPM
bodymap2_heart	0.00 RPM	5.93 RPM
bodymap2_kidney	0.00 RPM	22.03 RPM
bodymap2_liver	0.02 RPM	18.00 RPM
bodymap2_lung	0.11 RPM	8.32 RPM
bodymap2_lymph_node	0.35 RPM	19.26 RPM
bodymap2_ovary	0.15 RPM	26.16 RPM
bodymap2_prostate	0.03 RPM	25.11 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.46 RPM
bodymap2_testis	0.15 RPM	20.12 RPM
bodymap2_thyroid	0.11 RPM	15.67 RPM
bodymap2_white_blood_cells	0.26 RPM	20.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1799 was not detected

EST

No EST(s) were mapped for retro_hsap_1799 retrocopy.

TSS

No TSS is located nearby retro_hsap_1799 retrocopy 5' end.

Lab

retro_hsap_1799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1799 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1205
Pongo abelii	retro_pabe_1476

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799 ,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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