RetrogeneDB ID: retro_pabe_1894

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:16497614..16498480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSPPYG00000003296
• Aliases: None
• Description: Mitochondrial carrier homolog 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R5M0]

Sequence

>retro_pabe_1894
GCCAGTCAGATGCTCCTGGACTCCGGTCTCACCATCCTGTCCTAGCGACTCATGCACATGAAAGTGCTCATCCAGGTGGG
ATATGAGCCTCTTTCCCCAACAGGACAAAATATTTTGGGGTGGCAAGTATGTCAGCTTTCTGGTTTCTTTTGTTATGCTC
TGAACATTGCCAGCATTGACAGGAGGCGTGGGCTGTTCACAGGCTTAACTCCATGACTGCATTCAGGGGTCCTTGGAACT
GTGGTCCATGGTAAAATTTTACAGCATTACCAGGAGTGTGACAAGGGTGAGGAGTTAGGACCTGGATATGAACAGACAGA
AATCTCGTCTTCCTTTGACCAAATTATCAAGGAAACAACTCAAGAGATGATTGCTTGTTCTGCTGCTGCCCTCATCACGT
TCTTTCCATGTGCTCACTTTGTGATCTATGGCACAATTCACTGGGAGAGAATCCAAGTTCTGTGGACTTTGTGACACCAT
ACTAACCATTTATCAGGAAGAGGGTATCCTAGGATTTTTCCTAGGTCTTGTTCCTCACCTCCTAGGTGACATTATTTCTT
TGTGGCTGTGTGACTCACTAGCCTACCACCTTGTTGATACCCATGCAATGGACAGTGGGGTTTCTATCATGAATGAAACA
AAGAGTTATTCTCAAACTGTCACAGGATTTTTTTTGCCAGTATGTTGACCTACCCTTTGTGCTTGTCTCCAATCTTATGG
CTGTCAACAACTGTGGTCTTGCTGGTGGATGCCCTCCTTACTCCCCAATATATGCTTCTTGGATAGATTGCTGAGGCATG
CTACAAAGAGAGGAAATATGAGCCTAGGAAATAGCTTGGTTTTCCAGAGACAAGCCCTTTGGGAAG

Alignment

ORF - retro_pabe_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 75.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASQVLLGSGLTILSQPLMYVKVLIQVGYEPLPPTIGRNIFGRQVCQLPGLFSYAQHIASIDGRRGLFTGL
          ASQ.LL.SGLTILS..LM..KVLIQVGYEPL.PT.G.NI.G.QVCQL.G.F.YA..IASID.RRGLFTGL
Retrocopy ASQMLLDSGLTILS*RLMHMKVLIQVGYEPLSPT-GQNILGWQVCQLSGFFCYALNIASIDRRRGLFTGL

Parental  TPRLCSGVLGTVVHGKVLQHYQESDKGEELGPGNVQKEVSSSFDHVIKETTREMIARSAATLI-THPFHV
          TP.L.SGVLGTVVHGK.LQHYQE.DKGEELGPG..Q.E.SSSFD..IKE.T........A.......FHV
Retrocopy TP*LHSGVLGTVVHGKILQHYQECDKGEELGPGYEQTEISSSFDQIIKE-TTQEMIACSAAAL>SRSFHV

Parental  ITLRSMVQFIGRESKYCGLCDSIITIYREEGILGFFAGLVPRLLGDILSLWLCNSLAY-LVNTYALDSGV
          .TL.SM.QF.GRESK.CGLCD.I.TIY.EEGILGFF.GLVP.LLGDI.SLWLC.SLAY.LV.T.A.DSGV
Retrocopy LTL*SMAQFTGRESKFCGLCDTILTIYQEEGILGFFLGLVPHLLGDIISLWLCDSLAYHLVDTHAMDSGV

Parental  STMNEMKSYSQAVTGFFASM-LTYPFVLVSNLMAVNNCGLAGGCPPYSPIYTSWIDCWCMLQKE-GNMSR
          S.MNE.KSYSQ.VTG.........PFVLVSNLMAVNNCGLAGGCPPYSPIY.SWIDC..MLQ.E.GNMS.
Retrocopy SIMNETKSYSQTVTGXXXPV>VDLPFVLVSNLMAVNNCGLAGGCPPYSPIYASWIDC*GMLQRE<GNMSL

Parental  GNSLFF-RKVPFGK
          GNSL.F.R..PFGK
Retrocopy GNSLVF>RDKPFGK

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
SRP007412_brain_prefrontal_cortex	0.06 RPM	29.97 RPM
SRP007412_cerebellum	1.22 RPM	26.02 RPM
SRP007412_heart	0.00 RPM	24.99 RPM
SRP007412_kidney	0.20 RPM	66.46 RPM
SRP007412_liver	0.03 RPM	73.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1894 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1894 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894 , retro_pabe_872,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,