RetrogeneDB ID: retro_hsap_856

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:18617176..18617913(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000256282
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSG00000137409
• Aliases: MTCH1, CGI-64, PIG60, PSAP, SLC25A49
• Description: mitochondrial carrier 1 [Source:HGNC Symbol;Acc:17586]

Sequence

>retro_hsap_856
ATGGATGGCAAGACAGGGCTGTTCCGAGGTCTGAGCCCCCAACTGATGTGACCCCTCTCCTTTGTAACCAGGGGCAGCGT
GAAGGTTTTCCCTCCAGATGAAATCAAGCAGGTTTCCAATAAGGATGGATATGAAGACTTCTCTGAAGCAAGCAGTGAAG
GAGACCTCCTAGGGGATGATGATGCAGTGTGCGTCCTGTATGTTGGCCCACCCCCTGCATGCCATCTTGATGTGCTGCAT
GGTCTAATTTGTGGGATGGGAGGTTAAGTACAGTGGTGTGCTGAGCTCCACTGGGAAGATTTTCAAAGAGAAAGGGCCAC
TGGGATTCTTTGTTGGCTTGATCCCTCATGTCCCGGGTGAAGTAGTTTTCTTGTGAGGCTATAACCTGCTGGCCCACTTT
ATCAATGCCCACCTGGCGGATGACAGAGTGAGTGACACCTAGAGGGGCTGAGAAATGACCAGAATCGGGGTTCCCAGTTA
GGCCAGGCCCTGACCATCCAAAGCTACACCAAGTTTGTGATGGAGATCGCAGTGAGCATGCTGACCTACCCTTTCCTGCC
AGTTGGCAGCCTCATGGCTGTGAACAACTGCAGGCCGCAGGCTGGGCCCTCTCCTTACTCCCTGGTGTTCAAATCCTGGA
TTTACTGCTGTAAGTACCTGAGTGTGCAGGGCCAGCTCTTCTGAGGCTCCAGCCTGCTTTTCCCCACGTGTCATCAGGAT
CATGCTTTCGCCTGGAG

Alignment

ORF - retro_hsap_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.89 %
• Parental protein coverage: 63.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDGKIGLFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVSNKD-DMKTSLKKVVKETSYEMMMQCVSRM
          .DGK.GLFRGLSP.LM...LS.VTRGS.K.VFPPDEI.QVSNKD.DMKTSLK..VKETS..MMMQC.S.M
Retrocopy MDGKTGLFRGLSPQLM*-PLSFVTRGSVK-VFPPDEIKQVSNKD>DMKTSLKQAVKETS*GMMMQCASCM

Parental  LAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAY
          LAHPLH.I.M.CMV.FVG.E.KYSGVLSS.GKIFKE.G.LGFFVGLIPH..G.VVFL.G.NLLAHFINA.
Retrocopy LAHPLHAILMCCMV*FVGWEVKYSGVLSSTGKIFKEKGPLGFFVGLIPHVPGEVVFL*GYNLLAHFINAH

Parental  LVDDSVSDT-PGGLGNDQNPGSQFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPPY
          L.DD.VSDT...GL.NDQN.GSQ..QAL.I.SYTKFVM.IAVSMLTYPFL.VG.LMAVNNC..QAG..PY
Retrocopy LADDRVSDT<LEGLRNDQNRGSQLGQALTIQSYTKFVMEIAVSMLTYPFLPVGSLMAVNNCRPQAGPSPY

Parental  SPVFKSWIHCWKYLSVQGQLFRGSSLL-FRRVSSGSCFALE
          S.VFKSWI.C.KYLSVQGQLF.GSSLL.F..VSSGSCF.LE
Retrocopy SLVFKSWIYCCKYLSVQGQLF*GSSLL<FPHVSSGSCFRLE

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	87.46 RPM
bodymap2_adrenal	0.12 RPM	109.14 RPM
bodymap2_brain	0.00 RPM	172.82 RPM
bodymap2_breast	0.16 RPM	99.73 RPM
bodymap2_colon	0.00 RPM	147.61 RPM
bodymap2_heart	0.33 RPM	114.57 RPM
bodymap2_kidney	0.35 RPM	211.21 RPM
bodymap2_liver	0.00 RPM	61.57 RPM
bodymap2_lung	0.00 RPM	205.78 RPM
bodymap2_lymph_node	0.00 RPM	133.67 RPM
bodymap2_ovary	0.19 RPM	133.74 RPM
bodymap2_prostate	0.24 RPM	196.57 RPM
bodymap2_skeletal_muscle	0.00 RPM	58.35 RPM
bodymap2_testis	1.00 RPM	112.06 RPM
bodymap2_thyroid	0.06 RPM	409.17 RPM
bodymap2_white_blood_cells	0.00 RPM	69.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_856 was not detected

EST

No EST(s) were mapped for retro_hsap_856 retrocopy.

TSS

No TSS is located nearby retro_hsap_856 retrocopy 5' end.

Lab

retro_hsap_856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856 ,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101, retro_ttru_563,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.35 RPM
CEU_NA12873	0.35 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.15 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.34 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.50 RPM
GBR_HG00137	0.22 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.29 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.44 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.39 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.27 RPM
YRI_NA19093	0.16 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.31 RPM
YRI_NA19214	0.22 RPM
YRI_NA19223	0.28 RPM

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Indel association:

The presence of retro_hsap_856 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_856 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	11:18606213..18621800	100	100	100	100	100	99.17	100	100	99.44	100	100	100	100	100

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Indel #1, located at the genomic coordinates 11:18606213..18621800.