RetrogeneDB ID: retro_sscr_1163

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:68244853..68245179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000023323
• Aliases: None
• Description: None

Sequence

>retro_sscr_1163
ATAGGTGCCCCAGGCAGAAAGATTAATCGGCCCGAACAGAGCTAAAGGAGAAGCTGTTTCAAGAGATGGTGGGTGTTGAG
CTGAGGGCGGCGACCAAAGCACCATGTGGTTGGGGCTGCGATAGATGAAGGGCTGATCACACGGCACCCCTTCAAGAAGT
GGGCATCCAGTGAATGTGCCAACATTACTTTGTCTGGGAAGAAGTGCAAAAAACTCCTCCAGCAGATCTGGCTTACCTAG
AAAGAGAAAGCACCAATGGAGTGGAAGCCTCCTACAAGCCAGTCAAGACAACAGAGCCACAACCAAATTTGAAAAGGAAG
ACAAAA

Alignment

ORF - retro_sscr_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGAPGGKINRP-RTELKKKLF-KRRRVLSRERRLRHRVVGAVIDEGLITRHHLKKRASSARANITLSGKK
          .GAPG.KINRP.RTELK.KLF.KR..VLS..RR..H.VVGA.IDEGLITRH..KK.ASS..ANITLSGKK
Retrocopy IGAPGRKINRP<RTELKEKLF>KRWWVLS*GRRPKHHVVGAAIDEGLITRHPFKKWASSECANITLSGKK

Parental  RRKLLQQIRLAQKEKAAME-VEAPYKPARTSNSQPKLKKKPK
          ..KLLQQI.L..KEKA.ME.VEA.YKP..T...QP.LK.K.K
Retrocopy CKKLLQQIWLT*KEKAPME<VEASYKPVKTTEPQPNLKRKTK

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	13.94 RPM
SRP014902_testis	0.00 RPM	15.98 RPM
SRP018288_heart	0.00 RPM	10.35 RPM
SRP018288_kidney	0.00 RPM	26.10 RPM
SRP018288_liver	0.00 RPM	18.23 RPM
SRP018288_lung	0.00 RPM	24.23 RPM
SRP018856_adipose	0.00 RPM	22.21 RPM
SRP035408_brain	0.00 RPM	39.38 RPM
SRP035408_liver	0.00 RPM	27.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1163 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163 ,