RetrogeneDB ID: retro_sscr_1029

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:72083294..72083643(+)
• Located in intron of: ENSSSCG00000015286

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA5
• Ensembl ID: ENSSSCG00000016607
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 [Source:HGNC Symbol;Acc:7688]

Sequence

>retro_sscr_1029
ATGGAGGGGTGGCTGAAGAAGACCACTGGCCTTGTGGTACTGGCTATATGTGAAACTCCACATGAGAGGCTAAAAATATC
GTATACAAAGATTCTTGATGTTTTTTGGACAAATCCCTAAAAATGCAGCATATAGAAAGTATACAGAACAGATTACAAAT
GAGAAGCTGGGTATGGTTAAAGCATAATCAGATGTTTAAAAATGAGAAGAGCAACTTCAGGGTGACCAAATAGAAGAGGT
GATTCTTCAGGCTGAAAATGAACTAAGTCTGGCAAGAAAAGTGGTGCAGGAGAAGCCACGGGAGCCTTTAGTGGAAGAGC
CTACTGCCAACCAATGGAAATGGCCAATA

Alignment

ORF - retro_sscr_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLLKKTTGLVGLAVCETPHERLKILYTKILDVL-GQIPKNAAYRKYTEQITNEKLGMVKAEPDVKKLE
          M.G.LKKTTGLV.LA.CETPHERLKI.YTKILDV..GQIPKNAAYRKYTEQITNEKLGMVKA..DV.K.E
Retrocopy MEGWLKKTTGLVVLAICETPHERLKISYTKILDVF>GQIPKNAAYRKYTEQITNEKLGMVKA*SDV*K*E

Parental  EQLQGGQIEEVILQAENELSLARKMLRWKPWEPLVEEPPANQWKWPI
          EQLQG.QIEEVILQAENELSLARK....KP.EPLVEEP.ANQWKWPI
Retrocopy EQLQGDQIEEVILQAENELSLARKVVQEKPREPLVEEPTANQWKWPI

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	1.73 RPM
SRP014902_testis	0.14 RPM	6.08 RPM
SRP018288_heart	0.08 RPM	188.46 RPM
SRP018288_kidney	0.00 RPM	81.86 RPM
SRP018288_liver	0.00 RPM	39.02 RPM
SRP018288_lung	0.10 RPM	18.23 RPM
SRP018856_adipose	0.00 RPM	15.49 RPM
SRP035408_brain	0.00 RPM	93.57 RPM
SRP035408_liver	0.00 RPM	76.18 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1029 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1029 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004512	2 retrocopies	retro_amel_1543, retro_amel_695,
Bos taurus	ENSBTAG00000009334	5 retrocopies	retro_btau_1258, retro_btau_1613, retro_btau_537, retro_btau_808, retro_btau_950,
Canis familiaris	ENSCAFG00000025112	4 retrocopies	retro_cfam_302, retro_cfam_445, retro_cfam_882, retro_cfam_921,
Callithrix jacchus	ENSCJAG00000017449	1 retrocopy	retro_cjac_65,
Felis catus	ENSFCAG00000027125	5 retrocopies	retro_fcat_1081, retro_fcat_1278, retro_fcat_244, retro_fcat_550, retro_fcat_799,
Homo sapiens	ENSG00000128609	10 retrocopies	retro_hsap_1065, retro_hsap_1687, retro_hsap_2671, retro_hsap_3218, retro_hsap_3627, retro_hsap_3950, retro_hsap_3997, retro_hsap_4248, retro_hsap_745, retro_hsap_746,
Gorilla gorilla	ENSGGOG00000022922	9 retrocopies	retro_ggor_1264, retro_ggor_1864, retro_ggor_2185, retro_ggor_2447, retro_ggor_2654, retro_ggor_2683, retro_ggor_2848, retro_ggor_624, retro_ggor_840,
Loxodonta africana	ENSLAFG00000030971	1 retrocopy	retro_lafr_275,
Monodelphis domestica	ENSMODG00000015384	4 retrocopies	retro_mdom_1292, retro_mdom_1429, retro_mdom_1804, retro_mdom_525,
Mustela putorius furo	ENSMPUG00000006811	4 retrocopies	retro_mputfur_1151, retro_mputfur_1353, retro_mputfur_683, retro_mputfur_939,
Mus musculus	ENSMUSG00000023089	2 retrocopies	retro_mmus_2951, retro_mmus_853,
Otolemur garnettii	ENSOGAG00000033137	6 retrocopies	retro_ogar_1346, retro_ogar_1504, retro_ogar_1791, retro_ogar_2047, retro_ogar_2676, retro_ogar_649,
Pongo abelii	ENSPPYG00000017956	10 retrocopies	retro_pabe_1389, retro_pabe_2216, retro_pabe_2666, retro_pabe_2794, retro_pabe_2795, retro_pabe_2975, retro_pabe_3283, retro_pabe_3390, retro_pabe_3728, retro_pabe_887,
Pan troglodytes	ENSPTRG00000019637	10 retrocopies	retro_ptro_1141, retro_ptro_1800, retro_ptro_2235, retro_ptro_2452, retro_ptro_2682, retro_ptro_2714, retro_ptro_2888, retro_ptro_2937, retro_ptro_529, retro_ptro_725,
Rattus norvegicus	ENSRNOG00000005698	3 retrocopies	retro_rnor_1041, retro_rnor_2154, retro_rnor_2290,
Sus scrofa	ENSSSCG00000016607	2 retrocopies	retro_sscr_1029 , retro_sscr_693,
Ictidomys tridecemlineatus	ENSSTOG00000027404	1 retrocopy	retro_itri_911,