RetrogeneDB ID: retro_sscr_447

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:111929400..111930437(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSSSCG00000009223
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_sscr_447
ATGGCTCGACACTGCCTGGCAAAGACTTTAGCGACTGTGCCCCTTCTGTGGCCTTGGCCTCTGTGACAGTCAGGCCTGGC
AGCTGCCCCAGCACCTCCCCCGGCTGGAGCCCGTTTTCCTCACGTGTGTTCCCTCCAAACGTCATCATGTCAGTTTCAAA
TGGCGCTGTGAAGACGCCCCACAAGAAAGCCAGGACATCTCCGTACCCTGGCTCTAAAGTGGAGTGAAGCCAGGTCCCCG
ATGAGAAAGTGAGCTGGCAGGTTGAGTGGCCAGAGTACCAGCCTGTGGCGTACACTTCTGACTCCATCTTGACGAGACCC
AAGTGGGCAGACCCCCTGGTGGGTGAAAGGAACTTCTCTCCTAAATTTAATGAAAAAGATGGGCAGGTGGAGAGAAGGAG
CCAGAACGGCTGGTATAAGGTTAAAAATGGGAGACCTAGAAATCCTGTAGGTCAGACAGGGCTGGTTGGGCGAGGGCTTC
TGGGGCCTTGGGGTCCCAATCATGCTGCAGATCCCATCTTAACCAGGTGGAAAAAGGATGGCAAGGGCAATAAAGTTACC
CACCCTGTTTCTGGGAGAAACATCCTGCAATTTGTAGCCATCAAAAGGAAAGACTGTGGGGACTGGGCTATCCCAGGGGG
AATGGTAGATCCAGGAGAGAAGATTAGCACTACATTGAAAAGAGAATTTGGTGAGGAAGCCATGAACTCCTTACAGAAAC
CCAGAGCAGAAATACAGGCATTGGAGAAACAACTGCACAAACTATTCAGCCAGGAACACTTTGCGGTCTATAAAGGCTAT
GTGGATGATCCCTGGAACATGGATAATGCGTGGATAGAGACAGAGGCTGTGAACTACCACGATGAAACAGGCGAGGTAAT
GGACCATCTTCCTCTGGAAGCAGGCGATGATGCCAAGGAGGTGAGATAGGTGGACATTAATGATAAGCTCAAGCTTTATG
CCAGCCACTCCCAATTTAATCGACGTGTGTCTGAGAAACGAGGTGCCCACTGGAGGGAAGACGTGTACCCCGACTGC

Alignment

ORF - retro_sscr_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGRVLGKTLATVSL-SVALASVTLKSLGCCSLTTCRNSFLSCGFHLCSNMMSGSNGTKENSHNKARTSP
          MA...L.KTLATV.L.SVALASVT.....C.S.......F.S..F......MS.SNG.....H.KARTSP
Retrocopy MARHCLAKTLATVPL<SVALASVTVRPGSCPSTSPGWSPFSSRVFPP-NVIMSVSNGAVKTPHKKARTSP

Parental  YPGSKVHRSQVPNEKVGWLVEWQDYNPVEYTAVSVLAGPRWADPQISESNFSPKFNEKDGPIERKSQNGL
          YPGSKV..SQVP.EKV.W.VEW..Y.PV.YT..S.L..P.WADP...E.NFSPKFNEKDG..ER.SQNG.
Retrocopy YPGSKVE*SQVPDEKVSWQVEWPEYQPVAYTSDSILTRPKWADPLVGERNFSPKFNEKDGQVERRSQNGW

Parental  YEVENGRPRNPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDRSGNKIAHPVSGKNILQFVAIKRKDCGE
          Y.V.NGRPRNP.G.TGLVGRGLLG.WGPNHAADPI.TRWK.D..GNK..HPVSG.NILQFVAIKRKDCG.
Retrocopy YKVKNGRPRNPVGQTGLVGRGLLGPWGPNHAADPILTRWKKDGKGNKVTHPVSGRNILQFVAIKRKDCGD

Parental  WAIPGGMVDPGEKISATLKREFVEEALNSLQKSSAEKRELEKQLHKLFSQEHLVIYKGYVDDPRNTDNAW
          WAIPGGMVDPGEKIS.TLKREF.EEA.NSLQK..AE...LEKQLHKLFSQEH...YKGYVDDP.N.DNAW
Retrocopy WAIPGGMVDPGEKISTTLKREFGEEAMNSLQKPRAEIQALEKQLHKLFSQEHFAVYKGYVDDPWNMDNAW

Parental  METEAVNYHDETGEIMENLTLEAGDDAGKVKWVDINDKLKLYASHSQFIKLVAEKRDAHWSENPETDC
          .ETEAVNYHDETGE.M..L.LEAGDDA..V..VDINDKLKLYASHSQF...V.EKR.AHW.E....DC
Retrocopy IETEAVNYHDETGEVMDHLPLEAGDDAKEVR*VDINDKLKLYASHSQFNRRVSEKRGAHWREDVYPDC

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	21.10 RPM
SRP014902_testis	0.28 RPM	29.99 RPM
SRP018288_heart	0.05 RPM	44.37 RPM
SRP018288_kidney	0.10 RPM	111.41 RPM
SRP018288_liver	0.00 RPM	68.92 RPM
SRP018288_lung	0.00 RPM	63.84 RPM
SRP018856_adipose	0.17 RPM	42.81 RPM
SRP035408_brain	0.00 RPM	109.61 RPM
SRP035408_liver	0.00 RPM	241.42 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_447 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_447 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_709
Pan troglodytes	retro_ptro_506
Gorilla gorilla	retro_ggor_602
Pongo abelii	retro_pabe_613
Callithrix jacchus	retro_cjac_1047
Oryctolagus cuniculus	retro_ocun_990
Bos taurus	retro_btau_1112
Canis familiaris	retro_cfam_1271
Equus caballus	retro_ecab_123

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447 ,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,