RetrogeneDB ID: retro_sscr_346

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:149242901..149243428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC1
• Ensembl ID: ENSSSCG00000014296
• Aliases: None
• Description: Sus scrofa voltage-dependent anion channel 1 (VDAC1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_213960]

Sequence

>retro_sscr_346
ACAGGAAAGAAAAGTGGTAAAATCAAAGTCTTCTTATGAGAGAGTGTATAGACCTTGGTTGTGATGTTGACTTTGATTTT
GCTGGACCTGCAATCTGTGGTTCTGCTGTCTTTGGTTATGAGGGCTGGCTTGCTGGTGTCTTTGGTTATGACAGTGCCAA
ATCAAAGCTGACAAGGAATAACTATGCAGTGGGCTACAGGACTGGGGACTTCCAGCTACACACTGATGTCAATGATGGGA
CAGAATTTGGAGGATCAATTTATTGGAAAGTATGTGAAGATCTTGACACTTCAGTAAACCTTGCTTGGACATCAGCAACC
AACTACACTCGCTTTGGCACTGCAGCTAAGTATCATTTAGCTCCCACTGCTTCCATTTCTGCAAAAGTCAACAACTCTAG
TTTAATTGGAATGAGCAGCACTCAGACTCTGAGGCCTGGTGTAAAGCTCACACCATCTGCTCTGATAGATGGGAAGAGCA
TTAATGCTGGAGGCCACAAACTTCGGCTTGCCCTGGAGTTGGAGGCT

Alignment

ORF - retro_sscr_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.61 %
• Parental protein coverage: 62.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGKKNAKIKTGY-KREHVNLGCDVDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKT
          TGKK..KIK.....RE...LGCDVDFD.AGP.I.G..V.GYEGWLAG.......AKS..T..N.AVGY.T
Retrocopy TGKKSGKIKVFL<MRECIDLGCDVDFDFAGPAICGSAVFGYEGWLAGV-FGYDSAKSKLTRNNYAVGYRT

Parental  DEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGL
          ..FQLHT.VNDGTEFGGSIY.KV...L.T.VNLAWT.....TRFG.AAKY...P.A..SAKVNNSSLIG.
Retrocopy GDFQLHTDVNDGTEFGGSIYWKVCEDLDTSVNLAWTSATNYTRFGTAAKYHLAPTASISAKVNNSSLIGM

Parental  GYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA
          ..TQTL.PG.KLT.SAL.DGK..NAGGHKL.L.LE..A
Retrocopy SSTQTLRPGVKLTPSALIDGKSINAGGHKLRLALELEA

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	17.79 RPM	183.43 RPM
SRP014902_testis	13.58 RPM	112.31 RPM
SRP018288_heart	59.33 RPM	355.84 RPM
SRP018288_kidney	32.01 RPM	311.87 RPM
SRP018288_liver	12.95 RPM	161.67 RPM
SRP018288_lung	8.66 RPM	91.95 RPM
SRP018856_adipose	41.69 RPM	359.94 RPM
SRP035408_brain	22.26 RPM	194.69 RPM
SRP035408_liver	16.91 RPM	113.40 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_346 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000985	1 retrocopy	retro_cfam_1728,
Choloepus hoffmanni	ENSCHOG00000005631	6 retrocopies	retro_chof_1774, retro_chof_2420, retro_chof_813, retro_chof_858, retro_chof_866, retro_chof_99,
Callithrix jacchus	ENSCJAG00000013556	8 retrocopies	retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Cavia porcellus	ENSCPOG00000023840	2 retrocopies	retro_cpor_1061, retro_cpor_699,
Dasypus novemcinctus	ENSDNOG00000002680	5 retrocopies	retro_dnov_1367, retro_dnov_2117, retro_dnov_271, retro_dnov_30, retro_dnov_90,
Dipodomys ordii	ENSDORG00000000714	1 retrocopy	retro_dord_636,
Equus caballus	ENSECAG00000012365	2 retrocopies	retro_ecab_831, retro_ecab_832,
Felis catus	ENSFCAG00000008421	1 retrocopy	retro_fcat_1592,
Homo sapiens	ENSG00000213585	13 retrocopies	retro_hsap_1119, retro_hsap_1250, retro_hsap_2250, retro_hsap_2805, retro_hsap_308, retro_hsap_3527, retro_hsap_4287, retro_hsap_458, retro_hsap_4721, retro_hsap_4831, retro_hsap_4872, retro_hsap_4930, retro_hsap_847,
Gorilla gorilla	ENSGGOG00000010880	3 retrocopies	retro_ggor_693, retro_ggor_875, retro_ggor_981,
Loxodonta africana	ENSLAFG00000028818	1 retrocopy	retro_lafr_161,
Macaca mulatta	ENSMMUG00000016235	6 retrocopies	retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Monodelphis domestica	ENSMODG00000014157	1 retrocopy	retro_mdom_1120,
Mustela putorius furo	ENSMPUG00000010220	1 retrocopy	retro_mputfur_83,
Mus musculus	ENSMUSG00000020402	3 retrocopies	retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Nomascus leucogenys	ENSNLEG00000008023	11 retrocopies	retro_nleu_1044, retro_nleu_1318, retro_nleu_1561, retro_nleu_189, retro_nleu_1991, retro_nleu_2707, retro_nleu_3019, retro_nleu_433, retro_nleu_492, retro_nleu_873, retro_nleu_880,
Otolemur garnettii	ENSOGAG00000030742	2 retrocopies	retro_ogar_1197, retro_ogar_2876,
Ochotona princeps	ENSOPRG00000006605	2 retrocopies	retro_opri_397, retro_opri_467,
Pongo abelii	ENSPPYG00000015781	6 retrocopies	retro_pabe_1042, retro_pabe_1733, retro_pabe_273, retro_pabe_2913, retro_pabe_3756, retro_pabe_700,
Pan troglodytes	ENSPTRG00000017235	12 retrocopies	retro_ptro_1593, retro_ptro_1900, retro_ptro_249, retro_ptro_2905, retro_ptro_3138, retro_ptro_3215, retro_ptro_3246, retro_ptro_345, retro_ptro_588, retro_ptro_682, retro_ptro_84, retro_ptro_861,
Rattus norvegicus	ENSRNOG00000006375	8 retrocopies	retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Sus scrofa	ENSSSCG00000010320	2 retrocopies	retro_sscr_681, retro_sscr_791,
Sus scrofa	ENSSSCG00000014296	2 retrocopies	retro_sscr_346 , retro_sscr_801,
Ictidomys tridecemlineatus	ENSSTOG00000007764	3 retrocopies	retro_itri_1137, retro_itri_1506, retro_itri_693,
Tursiops truncatus	ENSTTRG00000016856	2 retrocopies	retro_ttru_1347, retro_ttru_752,
Vicugna pacos	ENSVPAG00000010448	1 retrocopy	retro_vpac_38,