RetrogeneDB ID: retro_sscr_987

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:147470029..147470718(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009258
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA10
• Ensembl ID: ENSSSCG00000012791
• Aliases: None
• Description: N(alpha)-acetyltransferase 10, NatA catalytic subunit [Source:HGNC Symbol;Acc:18704]

Sequence

>retro_sscr_987
ATGAACATCCGCAGTGCCCGGCCGGACGACCTGATGAACATGCAGCACTGCAACCTCCTCTGCCTTCCCGAGAACTACCA
GATGAAGTACTATTTCTACCACGGCCTCTCCTGGCCGCAGCTCTCGTACATCGCTGAGGACGAGGGCGGGAAGATTGTGG
GCTACGTCCTGGCCAAGATGGAAGAGGACCCCGACGACGTACCCCACGGACACATCACCTCCCTGGCCGTAAAGCGCTCG
CACCGGCGCCTCGGCCTGGCGCAGAAGCTGATGGACCAGGCCTCCCGGGCCATGGTGGAGAACTTCGGCGCCGAGTACGT
GTCTCTGCACGTGCGGAAGAGCAACCGGGCAGCCCTGCACCTCTATTCCAACACCCTCAACTTTGAGGTGAGCGAGGTGG
AGCCCAAATATTACGCAGACGGAGAAGACGCCTATGCCATGAAGCGGGACCTCTCGCAGATGGCCGGTGCGCTGAGGCGG
CAGCTGAGCTGAGGGCGAAGGGCGGCTCTGCGGTGCTGGGCCCCGGGGAGCGCCCGGAGACGCAGGGCAGCACACGCCCT
GCTTCCAGAGAGGCTGGTCAGGAGGAGAAGAACCCGGCCACTGACGGCAGTGGCAGTGACAAGGACCCCAGCCAGGCCAC
CGAAAGCACGGACGCCCAAGGCAGCTCAGAGGACTCCGACTCCACCTCC

Alignment

ORF - retro_sscr_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNIRNARPEDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDENGKIVGYVLAKMEEDPDDVPHG
          MNIR.ARP.DLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDE.GKIVGYVLAKMEEDPDDVPHG
Retrocopy MNIRSARPDDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDEGGKIVGYVLAKMEEDPDDVPHG

Parental  HITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSLHVRKSNRAALHLYSNTLNFQISEVEPKYYAD
          HITSLAVKRSHRRLGLAQKLMDQASRAM.ENF.A.YVSLHVRKSNRAALHLYSNTLNF..SEVEPKYYAD
Retrocopy HITSLAVKRSHRRLGLAQKLMDQASRAMVENFGAEYVSLHVRKSNRAALHLYSNTLNFEVSEVEPKYYAD

Parental  GEDAYAMKRDLTQMADELRRHL-ELKDKGRHVVLGSIENKADSKGNSLPSSGEACREEKGLAAEDSGGDS
          GEDAYAMKRDL.QMA..LRR.L.EL..KG...VLG..E......G...P.S.EA..EEK..A...SG.D.
Retrocopy GEDAYAMKRDLSQMAGALRRQL<ELRAKGGSAVLGPGE-RPETQGSTRPASREAGQEEKNPATDGSGSD-

Parental  KDLSEVSETTESTDVKDSSEASDSAS
          ......S..TESTD...SSE.SDS.S
Retrocopy ---KDPSQATESTDAQGSSEDSDSTS

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	0.53 RPM	69.42 RPM
SRP014902_testis	3.39 RPM	22.49 RPM
SRP018288_heart	0.08 RPM	15.48 RPM
SRP018288_kidney	0.49 RPM	42.16 RPM
SRP018288_liver	0.64 RPM	31.82 RPM
SRP018288_lung	0.00 RPM	17.21 RPM
SRP018856_adipose	0.00 RPM	35.07 RPM
SRP035408_brain	0.00 RPM	39.95 RPM
SRP035408_liver	0.00 RPM	38.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_987 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_987 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018457	1 retrocopy	retro_amel_162,
Bos taurus	ENSBTAG00000047702	1 retrocopy	retro_btau_177,
Canis familiaris	ENSCAFG00000019415	1 retrocopy	retro_cfam_167,
Callithrix jacchus	ENSCJAG00000014506	1 retrocopy	retro_cjac_132,
Cavia porcellus	ENSCPOG00000011495	1 retrocopy	retro_cpor_10,
Dipodomys ordii	ENSDORG00000002753	1 retrocopy	retro_dord_529,
Equus caballus	ENSECAG00000015203	1 retrocopy	retro_ecab_717,
Felis catus	ENSFCAG00000028705	1 retrocopy	retro_fcat_51,
Homo sapiens	ENSG00000102030	1 retrocopy	retro_hsap_13,
Gorilla gorilla	ENSGGOG00000009788	1 retrocopy	retro_ggor_196,
Macropus eugenii	ENSMEUG00000006054	2 retrocopies	retro_meug_1787, retro_meug_554,
Myotis lucifugus	ENSMLUG00000014267	1 retrocopy	retro_mluc_152,
Macaca mulatta	ENSMMUG00000000322	1 retrocopy	retro_mmul_21,
Mustela putorius furo	ENSMPUG00000008989	1 retrocopy	retro_mputfur_1424,
Mus musculus	ENSMUSG00000031388	1 retrocopy	retro_mmus_1416,
Nomascus leucogenys	ENSNLEG00000013724	1 retrocopy	retro_nleu_57,
Otolemur garnettii	ENSOGAG00000013263	1 retrocopy	retro_ogar_260,
Pongo abelii	ENSPPYG00000020861	1 retrocopy	retro_pabe_2530,
Pan troglodytes	ENSPTRG00000022419	1 retrocopy	retro_ptro_23,
Pteropus vampyrus	ENSPVAG00000000463	1 retrocopy	retro_pvam_1225,
Sarcophilus harrisii	ENSSHAG00000005952	1 retrocopy	retro_shar_362,
Sus scrofa	ENSSSCG00000012791	1 retrocopy	retro_sscr_987 ,
Ictidomys tridecemlineatus	ENSSTOG00000010237	1 retrocopy	retro_itri_1435,
Tursiops truncatus	ENSTTRG00000007455	1 retrocopy	retro_ttru_198,