RetrogeneDB ID: retro_hsap_2808

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:84740837..84741477(-)
• Located in intron of: ENSG00000242641

Retrocopy information

• Ensembl ID: ENSG00000241776
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSG00000163444
• Aliases: TMEM183A, C1orf37
• Description: transmembrane protein 183A [Source:HGNC Symbol;Acc:20173]

Sequence

>retro_hsap_2808
GGGACAGGTGAACACTGTGACATCATCAACAGCAGTGATGAGATGGATCCAGCTTAGGAGGAAAACATCCATGAGAGAAC
TTGTCTCTAGAAAAAAGAAAAGAAAAAGGAAACAGGAGACCTAGACGGGGCTGGAACAACATAGTGTCCCATGGATATTT
TACTATTTCCCGCCTCCTACGTCTGTCCTGAGGATATTGTGAAATTTTTCTTCATTTGTAAAAATGCCTGGACTGTCACT
TGTACTGCTGCCTTTTGGATCAGGTTATATCAAAAGCATTACATGCTGAATGCTTTTCAGCCTTTGCACCTGTGACCACA
GTCAATGGGGAAGCTGCAGTCTCTGGGCATATGTGATCCAGTCTCTGTACTGTATAAGTGATTTGTGGCTCAACTCTCCA
AGAATCCAGCCATTGCAGAAGCCACTCCCAGCACATTAAAGAATTCCAAATGCTTACTTTTCTGGTGCAGAATGGGCCCA
GAGAAGAACCGATGTGGGAAATCAACTTCAAGTTCAAAAAACAGGCCCCTACGTTAAAGAGCAATGTACGGGAGGATTGC
AGTCTCTCTTTCAGTATGAAGATGTTCACACCAACTCAGTCCAGGTGTGCTGCCTATTGTAGGTCACCACCCTCAATTTC

Alignment

ORF - retro_hsap_2808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.91 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAGEPCDIIDSSDEMD-AQEESIHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLLLASYIRPEDIVNFS
          G.GE.CDII.SSDEMD.A.EE.IHERT.............LDGAG....PMDI.L..ASY..PEDIV.F.
Retrocopy GTGEHCDIINSSDEMDPA*EENIHERTCLXXXXXXXXXGDLDGAGTT*CPMDILLFPASYVCPEDIVKFF

Parental  LICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLYHMYEPFAARISKNPAI
          .ICKNAWTVTCTAAFW.RLY..HY.L.A..PL.L.P.SM.KL..L..C...S....Y..F.A..SKNPAI
Retrocopy FICKNAWTVTCTAAFWIRLYQKHYMLNAFQPLHL*PQSMGKLQSLGICDPVSV--LYK*FVAQLSKNPAI

Parental  PESTPSTL-KNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKS-KCTGGLQPPVQYEDVHTNPDQDC
          .E.TPSTL.K....L.F......G.R.EPMWE.NFKFKKQ.P.LKS..CTGGLQ...QYEDVHTN..Q.C
Retrocopy AEATPSTL<KEFQMLTFLVQN--GPREEPMWEINFKFKKQAPTLKS<QCTGGLQSLFQYEDVHTNSVQVC

Parental  CLLQVTTLNF
          CLL.VTTLNF
Retrocopy CLL*VTTLNF

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	24.05 RPM
bodymap2_adrenal	0.00 RPM	36.11 RPM
bodymap2_brain	0.00 RPM	48.92 RPM
bodymap2_breast	0.00 RPM	28.04 RPM
bodymap2_colon	0.00 RPM	40.28 RPM
bodymap2_heart	0.00 RPM	11.34 RPM
bodymap2_kidney	0.00 RPM	34.41 RPM
bodymap2_liver	0.00 RPM	15.99 RPM
bodymap2_lung	0.00 RPM	30.98 RPM
bodymap2_lymph_node	0.00 RPM	39.11 RPM
bodymap2_ovary	0.00 RPM	33.54 RPM
bodymap2_prostate	0.00 RPM	42.12 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.78 RPM
bodymap2_testis	0.00 RPM	42.34 RPM
bodymap2_thyroid	0.00 RPM	38.10 RPM
bodymap2_white_blood_cells	0.00 RPM	40.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2808 was not detected

EST

No EST(s) were mapped for retro_hsap_2808 retrocopy.

TSS

No TSS is located nearby retro_hsap_2808 retrocopy 5' end.

Lab

retro_hsap_2808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2808 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1902

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808 , retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,

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).