RetrogeneDB ID: retro_pabe_1799

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:5243816..5244471(-)
• Located in intron of: ENSPPYG00000010707

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_1799
GTACACCCGGACTGGGTGGGTGAGGGCGACAAGGAGGACGCCACCCGCTGCTTCCAGATCCTGGGAAAAGTCTATTCCAT
TCTCAGTGACAGAGAACAGAGAGCAGTGTACGATGAGCAAAGAACAGTGGACGAAGGCTCTCCTGTGTTCACCCAAGACC
GAGACTGGGAGGCGTATTGGCGGCTACTCTTTAAAAAGATATCTTTAGAGGACATTCAAGCTTTTGAAAAGACATACAAA
GCTTTGGAAGAAGAGCTGGCTGATATTAAGCAGGCCTATCTGGACTTCAAGGGTGACATGGATCAGATCATGGAGTCTGT
GCTTTGCGTGCAGTACACAGAGGAACCCAGGATAAGGAATATCATTCAGCAAGCTATTGACGCCGGAGAGGTCCCATCCT
ATAATGCCTTTGTCAAAGAATCGAAACAAAAGATGAATGCAAGGAAAAGGAGGGCTCAGGAAGAGGCCAAAGAAGCAGAA
ATGAGCAGAAAGGAGTTGGGGCTTGATGAAGGCGTGGATAGCCTGAAGGCAGCCATTCAGAGCAGACAAAAGGATCGGCA
AAAGGAAATGGACAATTTTCTGGCTCAGATGGAAGCAAAGTACTTACTGCAAATCTTCCAAAGGAGGAGGGAAAAAATCT
GCTCTCAAGAAAGAA

Alignment

ORF - retro_pabe_1799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.84 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHPDRVGEGDKEDATRRFQILGKVYSVLSDREQRAVYDEQGTVDEDSPVLTQDRDWEAYWRLLFKKISLE
          VHPD.VGEGDKEDATR.FQILGKVYS.LSDREQRAVYDEQ.TVDE.SPV.TQDRDWEAYWRLLFKKIS..
Retrocopy VHPDWVGEGDKEDATRCFQILGKVYSILSDREQRAVYDEQRTVDEGSPVFTQDRDWEAYWRLLFKKISXX

Parental  DIQAFEKTFKGSEEELADIKQAYLDFRGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKE
          ...............LADIKQAYLDF.GDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKE
Retrocopy XXXXXXXXXXXXXXXLADIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKE

Parental  SKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEAKYCK-SSKGGG
          SKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEAKY....S..GG
Retrocopy SKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEAKYLL>KSSKGG

Parental  -KKSALKKE
          .KKSALKKE
Retrocopy GKKSALKKE

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	0.88 RPM	5.81 RPM
SRP007412_cerebellum	1.34 RPM	5.11 RPM
SRP007412_heart	0.48 RPM	5.72 RPM
SRP007412_kidney	0.53 RPM	6.96 RPM
SRP007412_liver	0.49 RPM	4.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1799 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1799 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2448
Pan troglodytes	retro_ptro_1414

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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,