RetrogeneDB ID: retro_sscr_279

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:30912039..30912942(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSSSCG00000013232
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_sscr_279
ATGGAAGACACAGCCAGTCAGGTGCTCCTAAGCTCCAGTCTCACCATCCTGTCCCAGCTGCTCATGTATGTGAAGGTGCT
CATCCAGGTGGGATATTATCCTCTTCCTCCAACAGCAGGACAGAATATTTTTGGGTGGCAAGTATGTCAGCTTCCTGGTC
TTTTTTGTTATGCTCAGCACCTTGCGAGCATTGATGGGCAGTGTGGATTGTTCACAGGCTTAACTCCAAGGCTATGTTGA
GGGGTCCTTGGAACTGTGGTCCACAGTGAAGTTTTACACCATTACCAGGAATGTGACAAGATTGAGGAGACAGGATCTGG
AAAGGTACAGAAAGAAGTTTCATCTTCCTTTGACTGAGTTATCAAGGAGACAGCTCAAGAGATAGTGGCTCATTCTATTG
CTACTGTCCTCACACATCCCTTCCATGTGATCACCCTGAGATATATGGTACAATTCATTGGCAGAGAAGCCAAGTACTGT
GAACTTTGTGACTCCACAGTAACTATCTATCGGGAAGAGGGTATCCTAGGATTTTTTGCAGGTCTTATTCCTTGCCTCCT
AGATGACATCATTTCTTTGTGGCTCTGTAACTCACTGGCCTACCCTGTCAATACCTATGCATTGGACAGTGGGGTTTCTA
CCATGAATGAAATGAAGAGATACCCAAGCTGTCACAGGATTTTTGCCAGTATGTTGACCTATCCTTTTGTGCTTGTCTCT
AAACTTATGGATGTCAACAACTGTGGGCTTGCTGGTGGATCCCCTCCTTATTCCCCAATATATACTTCTTGGATAGGTTA
CTGGTGCATGCTACAAAAAGAGTGAAATATAAGCCAAGGAAATAACTTGTTTTCCTGGAAGATCCCCTTTGGGAAGATTT
GTTGTGAACTGAGAATGTTAATT

Alignment

ORF - retro_sscr_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAASQVLLGSGLTILSQPLMYVKVLIQVGYEPLPPTIGRNIFGRQVCQLPGLFCYAQHIASIDGKRGL
          M.D.ASQVLL.S.LTILSQ.LMYVKVLIQVGY.PLPPT.G.NIFG.QVCQLPGLFCYAQH.ASIDG..GL
Retrocopy MEDTASQVLLSSSLTILSQLLMYVKVLIQVGYYPLPPTAGQNIFGWQVCQLPGLFCYAQHLASIDGQCGL

Parental  FTGLTPRLCSGVLGTVVHGKVLQHYQECDKVEETGSGNVQKEVSSSFDRVIKETTREMMARSAATLITHP
          FTGLTPRLC.GVLGTVVH..VL.HYQECDK.EETGSG.VQKEVSSSFD.VIKET..E..A.S.AT..THP
Retrocopy FTGLTPRLC*GVLGTVVHSEVLHHYQECDKIEETGSGKVQKEVSSSFD*VIKETAQEIVAHSIATVLTHP

Parental  FHVITLRSMVQFIGRESKYCGLCDSIVTIYREEGILGFFAGLIPRLLGDIISLWLCNSLAYLVNTYALDS
          FHVITLR.MVQFIGRE.KYC.LCDS.VTIYREEGILGFFAGLIP.LL.DIISLWLCNSLAY.VNTYALDS
Retrocopy FHVITLRYMVQFIGREAKYCELCDSTVTIYREEGILGFFAGLIPCLLDDIISLWLCNSLAYPVNTYALDS

Parental  GVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLMAVNNCGLAGGSPPYSPIYTSWIDCWCMLQKEGNMSR
          GVSTMNEMK.Y.......FASMLTYPFVLVS.LM.VNNCGLAGGSPPYSPIYTSWI..WCMLQKE.N.S.
Retrocopy GVSTMNEMKRY-PSCHRIFASMLTYPFVLVSKLMDVNNCGLAGGSPPYSPIYTSWIGYWCMLQKE*NISQ

Parental  GNSLFFRKVPFGKTYCCDLRMLI
          GN.LF..K.PFGK..CC.LRMLI
Retrocopy GNNLFSWKIPFGK-ICCELRMLI

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
SRP014902_placenta	0.00 RPM	19.11 RPM
SRP014902_testis	0.00 RPM	17.12 RPM
SRP018288_heart	0.00 RPM	72.66 RPM
SRP018288_kidney	0.00 RPM	124.61 RPM
SRP018288_liver	0.00 RPM	80.75 RPM
SRP018288_lung	0.00 RPM	28.10 RPM
SRP018856_adipose	0.00 RPM	22.65 RPM
SRP035408_brain	0.00 RPM	28.14 RPM
SRP035408_liver	0.00 RPM	61.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_279 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_279 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 30 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,
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,