RetrogeneDB ID: retro_pabe_1126

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:68785340..68785883(+)
• Located in intron of: ENSPPYG00000005930

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSPPYG00000002343
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 9 [Source:HGNC Symbol;Acc:19123]

Sequence

>retro_pabe_1126
CAGATCCTGGGAAAAGTCTATTCCGTTCTCAGTGACAAAGAACAGAGAGCAGTGTACGATGAGCAGGGAACAGTGGACGA
GGACTCTCCTGTGCTCACCCAAGACCTAGACTAGGAGGCGTACTGGCGGCTACTCTTTAAAAAGATATCTTTAGAGGACA
TTCAGTCTTTTGAAAAGACATACAAAGGTTCAGAAGAAGAGCTGGCTGATATTAAACAGGCCTATCTGGACTTCAAGGGT
GACATGGATCAGATCATGGAGTCTGTGCTTTGCGTGCAGTACACAGAGGAACCCAGGATAAGGAATATCGTTCAGCAAGC
TATTGACGCCAGAGGGGTCCAATCCTATAAGGCCTTTGTCAAAGAATCGAAACAAAAGATGAATGCAAGGAAAAGGAGGG
CTCAGGAAGAGGCCAAAGAAGCAGAAACGAGCAGAAAGGAGTTGGGGCTTGATGAAGGCGTGGATAACGTGAAGGCAGCC
ATTCAGAGCAGACAAAAGGAGCGGCAAAAGGAAATGGACAGTTTTCTGGCTCAGATGGAAGCA

Alignment

ORF - retro_pabe_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 82.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QILGKVYSVLSDREQRAVYDEQGTVDEDSPVLTQDRDWEAYWRLLFKKISLEDIQAFEKTFKGSEEELAD
          QILGKVYSVLSD.EQRAVYDEQGTVDEDSPVLTQD.D.EAYWRLLFKKISLEDIQ.FEKT.KGSEEELAD
Retrocopy QILGKVYSVLSDKEQRAVYDEQGTVDEDSPVLTQDLD*EAYWRLLFKKISLEDIQSFEKTYKGSEEELAD

Parental  IKQAYLDFRGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKESKQKMNARKRRAQEEAKE
          IKQAYLDF.GDMDQIMESVLCVQYTEEPRIRNI.QQAIDA..V.SY.AFVKESKQKMNARKRRAQEEAKE
Retrocopy IKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIVQQAIDARGVQSYKAFVKESKQKMNARKRRAQEEAKE

Parental  AEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEA
          AE.SRKELGLDEGVD..KAAIQSRQK.RQKEMD.FLAQMEA
Retrocopy AETSRKELGLDEGVDNVKAAIQSRQKERQKEMDSFLAQMEA

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	5.81 RPM
SRP007412_cerebellum	0.00 RPM	5.11 RPM
SRP007412_heart	0.00 RPM	5.72 RPM
SRP007412_kidney	0.00 RPM	6.96 RPM
SRP007412_liver	0.00 RPM	4.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1126 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1126 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1358
Pan troglodytes	retro_ptro_931
Gorilla gorilla	retro_ggor_1058

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016933	1 retrocopy	retro_amel_478,
Felis catus	ENSFCAG00000004448	1 retrocopy	retro_fcat_1310,
Homo sapiens	ENSG00000213551	2 retrocopies	retro_hsap_1358, retro_hsap_2448,
Gorilla gorilla	ENSGGOG00000015046	3 retrocopies	retro_ggor_1058, retro_ggor_1499, retro_ggor_1524,
Myotis lucifugus	ENSMLUG00000004539	3 retrocopies	retro_mluc_699, retro_mluc_700, retro_mluc_955,
Mustela putorius furo	ENSMPUG00000003792	1 retrocopy	retro_mputfur_727,
Nomascus leucogenys	ENSNLEG00000016595	1 retrocopy	retro_nleu_1394,
Otolemur garnettii	ENSOGAG00000003496	2 retrocopies	retro_ogar_1730, retro_ogar_1740,
Pongo abelii	ENSPPYG00000002343	2 retrocopies	retro_pabe_1126 , retro_pabe_1799,
Pan troglodytes	ENSPTRG00000034219	2 retrocopies	retro_ptro_1414, retro_ptro_931,
Ictidomys tridecemlineatus	ENSSTOG00000028067	1 retrocopy	retro_itri_413,
Tarsius syrichta	ENSTSYG00000011504	1 retrocopy	retro_tsyr_39,