RetrogeneDB ID: retro_pabe_3354

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:106674118..106674353(-)
• Located in intron of: ENSPPYG00000018787

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFM1
• Ensembl ID: ENSPPYG00000005293
• Aliases: None
• Description: ubiquitin-fold modifier 1 precursor [Source:RefSeq peptide;Acc:NP_001125310]

Sequence

>retro_pabe_3354
ATGTCAAAGGTTTCCTTTAAGATCACTCTGAGGTCTGACCCGCGGCTGGCGTACAAAGTACTCTGTTCCTGAGAGTACAC
CTTTCACAGCAGTCTTACAGTTTGCAACAGAAGAATTTCAAGTCTCTGCTGCAAGAAGTACAATTATTACCAATGATGGA
ATAGGAAAAAATCCTGCACAGACCGCTGGAAATGTTTTTGTAAAACATGGTTCAGAACTACGAATTATTCCTAGA

Alignment

ORF - retro_pabe_3354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKVSFKITLTSDPRLPYKVLSR-ESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKH
          MSKVSFKITL.SDPRL.YKVL...ESTPFTAVL.FA.EEF.V.AA.S.IITNDGIG.NPAQTAGNVF.KH
Retrocopy MSKVSFKITLRSDPRLAYKVLCS>ESTPFTAVLQFATEEFQVSAARSTIITNDGIGKNPAQTAGNVFVKH

Parental  GSELRIIPR
          GSELRIIPR
Retrocopy GSELRIIPR

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.11 RPM
SRP007412_cerebellum	0.12 RPM	1.95 RPM
SRP007412_heart	0.06 RPM	1.29 RPM
SRP007412_kidney	0.00 RPM	2.88 RPM
SRP007412_liver	0.06 RPM	4.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3354 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3354 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4098
Pan troglodytes	retro_ptro_2779
Gorilla gorilla	retro_ggor_2750
Callithrix jacchus	retro_cjac_1489

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006026	1 retrocopy	retro_cfam_1785,
Callithrix jacchus	ENSCJAG00000017903	4 retrocopies	retro_cjac_1489, retro_cjac_2545, retro_cjac_2807, retro_cjac_2872,
Equus caballus	ENSECAG00000014564	3 retrocopies	retro_ecab_293, retro_ecab_353, retro_ecab_392,
Erinaceus europaeus	ENSEEUG00000008471	1 retrocopy	retro_eeur_187,
Homo sapiens	ENSG00000120686	4 retrocopies	retro_hsap_1825, retro_hsap_2177, retro_hsap_4098, retro_hsap_4767,
Gorilla gorilla	ENSGGOG00000026214	3 retrocopies	retro_ggor_2168, retro_ggor_2750, retro_ggor_2970,
Macropus eugenii	ENSMEUG00000001660	2 retrocopies	retro_meug_1215, retro_meug_1615,
Microcebus murinus	ENSMICG00000008048	1 retrocopy	retro_mmur_1161,
Macaca mulatta	ENSMMUG00000014990	3 retrocopies	retro_mmul_1253, retro_mmul_2542, retro_mmul_908,
Mus musculus	ENSMUSG00000027746	2 retrocopies	retro_mmus_2246, retro_mmus_2311,
Nomascus leucogenys	ENSNLEG00000002556	3 retrocopies	retro_nleu_2973, retro_nleu_305, retro_nleu_567,
Otolemur garnettii	ENSOGAG00000007023	6 retrocopies	retro_ogar_2303, retro_ogar_2304, retro_ogar_2534, retro_ogar_2571, retro_ogar_617, retro_ogar_948,
Pongo abelii	ENSPPYG00000005293	4 retrocopies	retro_pabe_1492, retro_pabe_2061, retro_pabe_3354 , retro_pabe_3710,
Pan troglodytes	ENSPTRG00000040645	4 retrocopies	retro_ptro_1169, retro_ptro_1660, retro_ptro_2779, retro_ptro_3174,
Rattus norvegicus	ENSRNOG00000038176	2 retrocopies	retro_rnor_2201, retro_rnor_2202,
Sus scrofa	ENSSSCG00000021299	1 retrocopy	retro_sscr_584,
Ictidomys tridecemlineatus	ENSSTOG00000016449	2 retrocopies	retro_itri_1685, retro_itri_1746,
Tarsius syrichta	ENSTSYG00000011105	1 retrocopy	retro_tsyr_1979,
Tursiops truncatus	ENSTTRG00000015482	2 retrocopies	retro_ttru_1434, retro_ttru_518,