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 activity 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,