RetrogeneDB ID: retro_hsap_2541

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:17694399..17694644(+)
• Located in intron of: ENSG00000093072

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM32A
• Ensembl ID: ENSG00000105058
• Aliases: FAM32A, OTAG-12, OTAG12
• Description: family with sequence similarity 32, member A [Source:HGNC Symbol;Acc:24563]

Sequence

>retro_hsap_2541
GTGGATGCCTACGAGCAGGTACAAAAAGGACTTCTAAAGCTGAAAGGCGTCGCAGAGCTCAGAGTGACCAAGCGGAAGAA
GAAAAAGAAGGACAAAGACAAAGCTAAACTCCCGGAATCAATGGGAATGAACAAAAAGAATGAGGAGGAGAAGCAGCACG
GCCTGGACAAGTGGACCCCGGCCCGCGCAGCCTTTGAGAAAATGCAGGAGAAGCGGCAATGGAAAGGATCCTCAAGAAAG
CATCC

Alignment

ORF - retro_hsap_2541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 73.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAYEQVQKGPLKLKGVAELGVTKRKKKKKDKDKAKLLEAMGTSKKNEEEKRRGLDKRTPAQAAFEKMQE
          ..AYEQVQKG.LKLKGVAEL.VTKRKKKKKDKDKAKL.E.MG..KKNEEEK..GLDK.TPA.AAFEKMQE
Retrocopy VDAYEQVQKGLLKLKGVAELRVTKRKKKKKDKDKAKLPESMGMNKKNEEEKQHGLDKWTPARAAFEKMQE

Parental  KRQ-MERILKKAS
          KRQ.MERILKKAS
Retrocopy KRQ<MERILKKAS

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	32.78 RPM
bodymap2_adrenal	0.12 RPM	44.54 RPM
bodymap2_brain	0.02 RPM	21.38 RPM
bodymap2_breast	0.00 RPM	34.24 RPM
bodymap2_colon	0.00 RPM	31.88 RPM
bodymap2_heart	0.00 RPM	19.07 RPM
bodymap2_kidney	0.00 RPM	43.00 RPM
bodymap2_liver	0.00 RPM	39.01 RPM
bodymap2_lung	0.00 RPM	32.00 RPM
bodymap2_lymph_node	0.00 RPM	43.67 RPM
bodymap2_ovary	0.08 RPM	24.96 RPM
bodymap2_prostate	0.00 RPM	46.63 RPM
bodymap2_skeletal_muscle	0.00 RPM	18.32 RPM
bodymap2_testis	0.00 RPM	29.30 RPM
bodymap2_thyroid	0.00 RPM	39.92 RPM
bodymap2_white_blood_cells	0.12 RPM	81.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2541 was not detected

EST

No EST(s) were mapped for retro_hsap_2541 retrocopy.

TSS

No TSS is located nearby retro_hsap_2541 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: AAAGGGATACCTGTACTCGGATGC (24 nt long)
• Reverse primer: TTCTTGAGGATCCTTTCCATTGCCG (25 nt long)
• Anneling temperature: 58 °C
• (Expected) product size: 377
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2541 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1480

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Homo sapiens	ENSG00000105058	4 retrocopies	retro_hsap_1116, retro_hsap_1950, retro_hsap_2541 , retro_hsap_693,
Gorilla gorilla	ENSGGOG00000022418	4 retrocopies	retro_ggor_1420, retro_ggor_1587, retro_ggor_592, retro_ggor_872,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654,
Microcebus murinus	ENSMICG00000013721	3 retrocopies	retro_mmur_1449, retro_mmur_252, retro_mmur_500,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mustela putorius furo	ENSMPUG00000016048	1 retrocopy	retro_mputfur_1493,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017,
Nomascus leucogenys	ENSNLEG00000005441	3 retrocopies	retro_nleu_192, retro_nleu_2227, retro_nleu_2790,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Pan troglodytes	ENSPTRG00000010641	4 retrocopies	retro_ptro_1304, retro_ptro_1480, retro_ptro_497, retro_ptro_684,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,
Sus scrofa	ENSSSCG00000013855	2 retrocopies	retro_sscr_292, retro_sscr_870,
Tarsius syrichta	ENSTSYG00000009106	1 retrocopy	retro_tsyr_418,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.26 RPM

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Indel association:

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