RetrogeneDB ID: retro_sscr_842

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:58148978..58149411(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000003327
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000021591
• Aliases: None
• Description: Sus scrofa RNA binding motif (RNP1, RRM) protein 3 (RBM3), mRNA. [Source:RefSeq mRNA;Acc:NM_001243419]

Sequence

>retro_sscr_842
CTGTCCTCTGAGGAAGGGAAGCTCTCAGTGGGAGACCCCACCTCGACACCGAGGAGCAGGCGCCGGAGGACCCCCTGAGC
GGTCTCGGACCTATTTCTGCAGTGGTGGCTGTCGAGGACTGGGGGACCCAGAGGCGCCGGGTTTGGGCTCCATTCTCTTC
CCCAGTCCGGAGACCTGCTTCAGATGCAGCGAGAGCCACGAACAGAGAGTCTCTGGACGGTCGCCGGATCCGTGTGGACC
TCGCTGGCAAGTCGGCCCGGGGAACAAGAGGGGGTGCCTTTGGGGCACACGGCTGTGGTCGTGGCTCCTCTAGAGGTGGA
GGGGACCAGAGCCATGCAAGTGGCAGATACGACGTCGACCAGGAGGACAGGGATACGGATGTGGACGTGGAAGGGCCAGC
GCCTACGGCGGCGGAAATTACGGGGAAAATGAC

Alignment

ORF - retro_sscr_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.42 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGL-NFNTDEQALEDHFSSFGPISEVVVVKDRETQRSR-GFGFITFTNPEH-ASNAMRAM
          .SSEEGKL.VG......T.EQA.ED..S..GPIS.VV.V.D..TQR.R.G.G.I.F..PE..AS.A.RA.
Retrocopy LSSEEGKLSVGDP<HLDTEEQAPEDPLSGLGPISAVVAVEDWGTQRRR<GLGSILFPSPET>ASDAARAT

Parental  NGESLDGRQIRVDHAGKSARGTRGGAFGAR--GRGYSRGGGDQGYGNGRYD-SRPGGYGYGYGYGRSRDY
          N.ESLDGR.IRVD.AGKSARGTRGGAFGA...GRG.SRGGGDQ....GRYD..RPGG.GYG.G.GR...Y
Retrocopy NRESLDGRRIRVDLAGKSARGTRGGAFGAHGCGRGSSRGGGDQSHASGRYD<RRPGGQGYGCGRGRASAY

Parental  GSRSQGSYD
          G....G..D
Retrocopy GGGNYGEND

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	30.66 RPM
SRP014902_testis	0.00 RPM	84.73 RPM
SRP018288_heart	0.00 RPM	48.41 RPM
SRP018288_kidney	0.00 RPM	45.31 RPM
SRP018288_liver	0.00 RPM	22.87 RPM
SRP018288_lung	0.00 RPM	56.11 RPM
SRP018856_adipose	0.00 RPM	58.22 RPM
SRP035408_brain	0.03 RPM	25.92 RPM
SRP035408_liver	0.00 RPM	16.53 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_842 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842 ,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,