RetrogeneDB ID: retro_sscr_789

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:1444806..1445478(+)
• Located in intron of: ENSSSCG00000000017

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1E1
• Ensembl ID: ENSSSCG00000000767
• Aliases: None
• Description: None

Sequence

>retro_sscr_789
CTCAGCAATGCCCACGTGCAGAAGCAGATTAAGCACATGATGGCTTTTATTGAACAAGAAGCCAATGAGAAAGCAGAAGA
AATAGATGTGAAGGCAGAAGAGGAGTTCAACATTGAGAAAAGTCGTCTTGTACAAACCCAGAGACTGGAGATTATGGAAT
ATTACGAGAAAAAAGAAAAGCAGATTGAACAGCAGAAGGAAATTCAAATGTCTAATTTGATGAATCAAGCGAGGCTCAAA
GTCCTCAGAGCCAGCAGTGACCTCGTCACAGACCTGCTAAATGAAGCAAAACAGAGACTCAGCAAAGTGGTGAAAGATAC
AACCAGGTGCTGAGTGTCGTCGGATGGAGTGGTCCTCCAGGCTTTGTACCAGTTGTTGAAGCCCCAAAGGTTCCTTCGCT
GCAGGAAACAAGATTTCCCGCTGGTAAAGGCTGCTGTGCAGGAAGCCATCCCTGTTTACAAAATCGCCACCAAAAGAGAT
GTCGCTGTCCAGACTGATCGGGAGGCCTACCTGCCTGAGGAAGTAGCTGGCAGGGTTGAGATCTGTAACGGGGATCGAAA
AATCAAGGTTTCCAATACCTTGGAGAACCGGCTGGGCCTCATAGCTCAGCAGATGGTGCCAGAGGTGCGGGGAGCCTTGT
TTGGTGCCAATGCCAACAGGAGGTTTTTGGAC

Alignment

ORF - retro_sscr_789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQM
          LS.A.VQKQIKHMMAFIEQEANEKAEEID.KAEEEFNIEK.RLVQTQRL.IMEYYEKKEKQIEQQK.IQM
Retrocopy LSNAHVQKQIKHMMAFIEQEANEKAEEIDVKAEEEFNIEKSRLVQTQRLEIMEYYEKKEKQIEQQKEIQM

Parental  SNLMNQARLKVLRARDDLITDLLNEAKQRLGKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFP
          SNLMNQARLKVLRA..DL.TDLLNEAKQRL.KVVKDTTR..V..DG.VLQ.LYQLL.P....RCRKQDFP
Retrocopy SNLMNQARLKVLRASSDLVTDLLNEAKQRLSKVVKDTTRC*VSSDGVVLQALYQLLKPQRFLRCRKQDFP

Parental  LVKAAVQKAIPVYKIATKRDVDVQIDQEAYLPEEIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVR
          LVKAAVQ.AIPVYKIATKRDV.VQ.D.EAYLPEE.AG.VEI.NGDRKIKVSNTLE.RL.LIAQQM.PEVR
Retrocopy LVKAAVQEAIPVYKIATKRDVAVQTDREAYLPEEVAGRVEICNGDRKIKVSNTLENRLGLIAQQMVPEVR

Parental  GALFGANANRKFLD
          GALFGANANR.FLD
Retrocopy GALFGANANRRFLD

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	112.95 RPM
SRP014902_testis	0.00 RPM	51.35 RPM
SRP018288_heart	0.00 RPM	74.89 RPM
SRP018288_kidney	0.00 RPM	188.64 RPM
SRP018288_liver	0.00 RPM	52.29 RPM
SRP018288_lung	0.00 RPM	95.21 RPM
SRP018856_adipose	0.00 RPM	175.90 RPM
SRP035408_brain	0.00 RPM	314.81 RPM
SRP035408_liver	0.00 RPM	104.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_789 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_789 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017489	2 retrocopies	retro_amel_116, retro_amel_1502,
Bos taurus	ENSBTAG00000014238	1 retrocopy	retro_btau_244,
Canis familiaris	ENSCAFG00000016151	7 retrocopies	retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus	ENSCJAG00000017277	1 retrocopy	retro_cjac_1160,
Cavia porcellus	ENSCPOG00000024559	3 retrocopies	retro_cpor_172, retro_cpor_580, retro_cpor_76,
Equus caballus	ENSECAG00000016487	2 retrocopies	retro_ecab_165, retro_ecab_84,
Echinops telfairi	ENSETEG00000019283	2 retrocopies	retro_etel_1384, retro_etel_6,
Felis catus	ENSFCAG00000008081	4 retrocopies	retro_fcat_153, retro_fcat_602, retro_fcat_61, retro_fcat_654,
Homo sapiens	ENSG00000131100	3 retrocopies	retro_hsap_1126, retro_hsap_145, retro_hsap_21,
Gorilla gorilla	ENSGGOG00000015027	2 retrocopies	retro_ggor_105, retro_ggor_235,
Loxodonta africana	ENSLAFG00000003802	4 retrocopies	retro_lafr_1220, retro_lafr_123, retro_lafr_134, retro_lafr_742,
Microcebus murinus	ENSMICG00000010643	6 retrocopies	retro_mmur_1214, retro_mmur_1234, retro_mmur_813, retro_mmur_886, retro_mmur_971, retro_mmur_978,
Myotis lucifugus	ENSMLUG00000014876	2 retrocopies	retro_mluc_312, retro_mluc_57,
Macaca mulatta	ENSMMUG00000021477	4 retrocopies	retro_mmul_1102, retro_mmul_139, retro_mmul_370, retro_mmul_873,
Monodelphis domestica	ENSMODG00000018452	4 retrocopies	retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furo	ENSMPUG00000018109	2 retrocopies	retro_mputfur_23, retro_mputfur_4,
Mus musculus	ENSMUSG00000019210	1 retrocopy	retro_mmus_122,
Nomascus leucogenys	ENSNLEG00000007839	1 retrocopy	retro_nleu_18,
Otolemur garnettii	ENSOGAG00000013886	5 retrocopies	retro_ogar_1255, retro_ogar_1401, retro_ogar_2930, retro_ogar_6, retro_ogar_839,
Procavia capensis	ENSPCAG00000016094	1 retrocopy	retro_pcap_455,
Pongo abelii	ENSPPYG00000011560	1 retrocopy	retro_pabe_189,
Rattus norvegicus	ENSRNOG00000011905	1 retrocopy	retro_rnor_383,
Sarcophilus harrisii	ENSSHAG00000008300	2 retrocopies	retro_shar_501, retro_shar_780,
Sus scrofa	ENSSSCG00000000767	3 retrocopies	retro_sscr_788, retro_sscr_789 , retro_sscr_83,
Ictidomys tridecemlineatus	ENSSTOG00000022031	3 retrocopies	retro_itri_579, retro_itri_630, retro_itri_64,
Tarsius syrichta	ENSTSYG00000010679	5 retrocopies	retro_tsyr_1093, retro_tsyr_1812, retro_tsyr_23, retro_tsyr_532, retro_tsyr_797,
Tursiops truncatus	ENSTTRG00000015931	1 retrocopy	retro_ttru_1,