RetrogeneDB ID: retro_hsap_3565

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:25679293..25679651(-)
• Located in intron of: ENSG00000079689

Retrocopy information

• Ensembl ID: ENSG00000217408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSG00000169230
• Aliases: PRELID1, PRELI, PX19, SBBI12
• Description: PRELI domain containing 1 [Source:HGNC Symbol;Acc:30255]

Sequence

>retro_hsap_3565
ATGATGAAGTATTCCTAGGCCAGAACAGGCTCCAGAATTTCTGAAACCAAATGTTCACTGCCTTGTGACATTGGTACTCA
AATCCCTATAGCAAACATGCTCTGACCAAAAACACAGAATATGAGGAGGTGACCCCTGCCCAGAAGCTCCTGTCCCAGTG
ACTCCTGACCAAGACCAGTGGGATGTCCTGCTGGGCTGAGTGGCTATTTCTTGCCAATGATGCTCACCCAGTGTCCATCC
TGGAGGACTCTACTGGGCACCCACACAATCAGAAGTGACCACCTTCACCTGTAGCATCAACCATGCCCAGCTGATGGTGG
TGGAGGGACGATGTATTTACTGTGTGAACTCTGAGAAC

Alignment

ORF - retro_hsap_3565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVKY-FLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERL
          M.KY.FLGQ..L.....Q.F.A....Y.NPYSKH.LT......EVTP.QKLLS..LLTKT..M..WAE.L
Retrocopy MMKY<FLGQNRLQNF*NQMFTAL*HWYSNPYSKHALTKNTEYEEVTPAQKLLSQ*LLTKTSGMSCWAEWL

Parental  FPANVAHSVYVLEDSIVDPQNQ-TMTTFTWNINHARLMVVEERCVYCVNSDN
          F.AN.AH.V..LEDS...P.NQ...TTFT..INHA.LMVVE.RC.YCVNS.N
Retrocopy FLANDAHPVSILEDSTGHPHNQ<EVTTFTCSINHAQLMVVEGRCIYCVNSEN

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	16.04 RPM
bodymap2_adrenal	0.00 RPM	27.14 RPM
bodymap2_brain	0.00 RPM	7.29 RPM
bodymap2_breast	0.00 RPM	12.43 RPM
bodymap2_colon	0.00 RPM	15.29 RPM
bodymap2_heart	0.00 RPM	3.71 RPM
bodymap2_kidney	0.00 RPM	15.65 RPM
bodymap2_liver	0.00 RPM	15.27 RPM
bodymap2_lung	0.00 RPM	19.06 RPM
bodymap2_lymph_node	0.00 RPM	17.60 RPM
bodymap2_ovary	0.00 RPM	12.57 RPM
bodymap2_prostate	0.00 RPM	14.39 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.46 RPM
bodymap2_testis	0.00 RPM	13.71 RPM
bodymap2_thyroid	0.00 RPM	11.96 RPM
bodymap2_white_blood_cells	0.00 RPM	43.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3565 was not detected

EST

No EST(s) were mapped for retro_hsap_3565 retrocopy.

TSS

No TSS is located nearby retro_hsap_3565 retrocopy 5' end.

Lab

retro_hsap_3565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3565 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2404
Macaca mulatta	retro_mmul_1822
Callithrix jacchus	retro_cjac_2401

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005009	2 retrocopies	retro_btau_1727, retro_btau_962,
Canis familiaris	ENSCAFG00000016443	2 retrocopies	retro_cfam_2055, retro_cfam_349,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Homo sapiens	ENSG00000169230	7 retrocopies	retro_hsap_1550, retro_hsap_2269, retro_hsap_249, retro_hsap_302, retro_hsap_3518, retro_hsap_3565 , retro_hsap_579,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mustela putorius furo	ENSMPUG00000012226	1 retrocopy	retro_mputfur_579,
Nomascus leucogenys	ENSNLEG00000012714	5 retrocopies	retro_nleu_1382, retro_nleu_2395, retro_nleu_2400, retro_nleu_803, retro_nleu_857,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Pongo abelii	ENSPPYG00000016086	7 retrocopies	retro_pabe_1283, retro_pabe_1696, retro_pabe_1699, retro_pabe_2907, retro_pabe_377, retro_pabe_409, retro_pabe_608,
Sus scrofa	ENSSSCG00000014042	4 retrocopies	retro_sscr_372, retro_sscr_794, retro_sscr_795, retro_sscr_811,
Tupaia belangeri	ENSTBEG00000006445	1 retrocopy	retro_tbel_3855,
Tursiops truncatus	ENSTTRG00000009571	1 retrocopy	retro_ttru_1886,

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).