RetrogeneDB ID: retro_hsap_522

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:228302698..228303157(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224566
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSG00000166797
• Aliases: None
• Description: family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235]

Sequence

>retro_hsap_522
CTGCTTTCCTGGACACTGAGCAGAATCCTGTGGCTCTCGGGCCTCTTTGAGTGGGGAGCTGCCCGGCAGCCCCGGATCAT
GGAAGAGAAAGTGCTAGAGGTTTATGATTTGATTCGAACTATCTGGGACCCAGAAAAGCCCAATACTTTAGAAGAACTGG
AATTGGTAACGGAAAGTTATATGGAAGTTCAGGAGATAAATGAAGAAGACTATCTGGTTATTATCAAGTTTACACCAAGA
GTACCTCATTGATATTTGGCGATTCTTATGGGGCTGTGCTTAAGAATAAAACTTCAGCAGTGTTTACCATTTAAACATAA
GTTGGAAATCTACATTTCTGAAGGAACCCACTCAACAGAAGATATAAGTATGCAGATAAACAACAAAGAGCAAGTGGAGG
CTGCAATGGAAAACCCCAGCTTATGGGAAATTGCGGAACAGTGTGTCCTTGAACCTGAC

Alignment

ORF - retro_hsap_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.47 %
• Parental protein coverage: 96.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLSWTLSRVLWLSGLSEPGAARQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVSESCVEVQEINEEE
          LLSWTLSR.LWLSGL.E.GAARQPRIMEEK.LEVYDLIRTI.DPEKPNTLEELE.V.ES..EVQEINEE.
Retrocopy LLSWTLSRILWLSGLFEWGAARQPRIMEEKVLEVYDLIRTIWDPEKPNTLEELELVTESYMEVQEINEED

Parental  YLVIIRFTPTVPHCSLATLIGLCLRVKLQRCLPFKHKLEIYISEGTHSTEEDINKQINDKERVAAAMENP
          YLVII.FTP.VPH..LA.L.GLCLR.KLQ.CLPFKHKLEIYISEGTHSTE.DI..QIN.KE.V.AAMENP
Retrocopy YLVIIKFTPRVPH*YLAILMGLCLRIKLQQCLPFKHKLEIYISEGTHSTE-DISMQINNKEQVEAAMENP

Parental  NLREIVEQCVLEPD
          .L.EI.EQCVLEPD
Retrocopy SLWEIAEQCVLEPD

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	16.82 RPM
bodymap2_adrenal	0.16 RPM	33.39 RPM
bodymap2_brain	0.14 RPM	13.17 RPM
bodymap2_breast	0.23 RPM	17.37 RPM
bodymap2_colon	0.15 RPM	25.99 RPM
bodymap2_heart	0.00 RPM	24.17 RPM
bodymap2_kidney	0.00 RPM	53.27 RPM
bodymap2_liver	0.00 RPM	78.07 RPM
bodymap2_lung	0.11 RPM	21.66 RPM
bodymap2_lymph_node	0.15 RPM	42.58 RPM
bodymap2_ovary	0.17 RPM	13.80 RPM
bodymap2_prostate	0.12 RPM	20.04 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.98 RPM
bodymap2_testis	0.08 RPM	24.62 RPM
bodymap2_thyroid	0.04 RPM	55.12 RPM
bodymap2_white_blood_cells	0.06 RPM	50.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_522 was not detected

EST

No EST(s) were mapped for retro_hsap_522 retrocopy.

TSS

No TSS is located nearby retro_hsap_522 retrocopy 5' end.

Lab

retro_hsap_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_522 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_390
Gorilla gorilla	retro_ggor_481
Pongo abelii	retro_pabe_224

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522 ,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.43 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.34 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	0.27 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.33 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.17 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.17 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.28 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.67 RPM
GBR_HG00131	0.37 RPM
GBR_HG00133	0.24 RPM
GBR_HG00134	0.41 RPM
GBR_HG00137	0.27 RPM
GBR_HG00142	0.33 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.29 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.26 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.57 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.34 RPM

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Indel association:

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