RetrogeneDB ID: retro_sscr_978

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:112091166..112091657(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSSSCG00000005959
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_sscr_978
AGAACAACACAGGGTCGTATGAGAATTAATAATGTTCCAGAAGAAGGAGAAAATGAAGTAAATAATGAATTGGAAAATCG
AATATCTTTGTTTTTGCTGAGGCAATCCCAATACTGAAAACCTTAAGTGATGCCACAAAAAAATTTGTATCAGAGAATAA
AAAATTACCAATAGAAAATACTACAGATTGTCTAAGCACCATGGCTAGTGTGTGCAGAGTCATGCTTGAAACACTGGAAT
ACAGAAGTCGATTTACAGATTAAGAGACAGTGTCATTCTGCTTAAGGGTAATGGTGAACATAATACTCTATGACCACATA
CATCAAGTGGGAGCATTTGCCAAAACTTCAAAAATTGATATGAAAGGTTGTATCAAAGCTCTTAAGGACCAGCCTCCTAA
TAGTGTAGACGGTCTTCCTCATGCTCTCAGGTACACAATTAAACATTAGAATGATAGGACTACCTCCAAGCAGATTAAAT
TCATGCTGCGT

Alignment

ORF - retro_sscr_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRTLSRMRINNVPAEGENEVNNELANRMSLF-YAEATPMLKTLSDATTKFVSENKNLPIENTTDCLSTMA
          R.T..RMRINNVP.EGENEVNNEL.NR.SLF..AEA.P.LKTLSDAT.KFVSENK.LPIENTTDCLSTMA
Retrocopy RTTQGRMRINNVPEEGENEVNNELENRISLF<FAEAIPILKTLSDATKKFVSENKKLPIENTTDCLSTMA

Parental  SVCRVMLETPEYRSRFTNEETVSFCLRVMVGVIILYDHVHPVGAFAKTSKIDMKGCIKVLKDQPPNSVEG
          SVCRVMLET.EYRSRFT..ETVSFCLRVMV..IILYDH.H.VGAFAKTSKIDMKGCIK.LKDQPPNSV.G
Retrocopy SVCRVMLETLEYRSRFTD*ETVSFCLRVMVN-IILYDHIHQVGAFAKTSKIDMKGCIKALKDQPPNSVDG

Parental  LLNALRYTTKHLNDETTSKQIKSMLQ
          L..ALRYT.KH.ND.TTSKQIK.ML.
Retrocopy LPHALRYTIKH*NDRTTSKQIKFMLR

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	16.72 RPM
SRP014902_testis	0.00 RPM	19.66 RPM
SRP018288_heart	0.00 RPM	15.32 RPM
SRP018288_kidney	0.00 RPM	10.24 RPM
SRP018288_liver	0.00 RPM	7.84 RPM
SRP018288_lung	0.00 RPM	45.31 RPM
SRP018856_adipose	0.00 RPM	11.02 RPM
SRP035408_brain	0.06 RPM	43.45 RPM
SRP035408_liver	0.00 RPM	15.24 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_978 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978 ,