RetrogeneDB ID: retro_sscr_544

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:34160641..34160860(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016886
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBL5
• Ensembl ID: ENSSSCG00000023331
• Aliases: None
• Description: Sus scrofa ubiquitin-like 5 (UBL5), mRNA. [Source:RefSeq mRNA;Acc:NM_001204116]

Sequence

>retro_sscr_544
ATGATCGAGGTTGTTTGCAACGACCGTCTGGGGAAGAAGGTCCGCGTTAAATGCAATACGGATGACACCATCGGGGACCT
TAAGAAGCTGATCGCAGCCCAAACTGGCACCCGTTGGAACAAGATCATATTGAAGAAGTGGTACACGATTTTTAAGGACC
ACGTGTCTCTGGGGGAGTATGAAATCCATGATGGGATGAACCTGGAGCTTTATTACCAA

Alignment

ORF - retro_sscr_544 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLEL
          MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKI.LKKWYTIFKDHVSLG.YEIHDGMNLEL
Retrocopy MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIILKKWYTIFKDHVSLGEYEIHDGMNLEL

Parental  YYQ
          YYQ
Retrocopy YYQ

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	3.45 RPM	23.76 RPM
SRP014902_testis	3.54 RPM	36.35 RPM
SRP018288_heart	6.26 RPM	46.70 RPM
SRP018288_kidney	21.97 RPM	70.53 RPM
SRP018288_liver	14.87 RPM	42.22 RPM
SRP018288_lung	4.89 RPM	63.44 RPM
SRP018856_adipose	10.93 RPM	67.96 RPM
SRP035408_brain	12.45 RPM	38.02 RPM
SRP035408_liver	12.33 RPM	27.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_544 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_544 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006097	1 retrocopy	retro_cjac_1394,
Dasypus novemcinctus	ENSDNOG00000006384	5 retrocopies	retro_dnov_1858, retro_dnov_196, retro_dnov_2470, retro_dnov_2590, retro_dnov_860,
Homo sapiens	ENSG00000198258	3 retrocopies	retro_hsap_1821, retro_hsap_2798, retro_hsap_3154,
Gorilla gorilla	ENSGGOG00000005999	1 retrocopy	retro_ggor_173,
Loxodonta africana	ENSLAFG00000012892	2 retrocopies	retro_lafr_1245, retro_lafr_699,
Macropus eugenii	ENSMEUG00000015506	2 retrocopies	retro_meug_300, retro_meug_304,
Myotis lucifugus	ENSMLUG00000027369	2 retrocopies	retro_mluc_1516, retro_mluc_1766,
Macaca mulatta	ENSMMUG00000007877	2 retrocopies	retro_mmul_1437, retro_mmul_1996,
Mus musculus	ENSMUSG00000084786	1 retrocopy	retro_mmus_98,
Pongo abelii	ENSPPYG00000009536	3 retrocopies	retro_pabe_1489, retro_pabe_2226, retro_pabe_2814,
Pan troglodytes	ENSPTRG00000010451	3 retrocopies	retro_ptro_1170, retro_ptro_1895, retro_ptro_2280,
Pteropus vampyrus	ENSPVAG00000008628	1 retrocopy	retro_pvam_1461,
Sarcophilus harrisii	ENSSHAG00000010974	1 retrocopy	retro_shar_753,
Sus scrofa	ENSSSCG00000023331	2 retrocopies	retro_sscr_544 , retro_sscr_608,
Tursiops truncatus	ENSTTRG00000008535	1 retrocopy	retro_ttru_166,