RetrogeneDB ID: retro_ptro_1414

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:10498096..10498834(-)
• Located in intron of: ENSPTRG00000013248

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSPTRG00000034219
• Aliases: None
• Description: None

Sequence

>retro_ptro_1414
CTTTACTGGGTGCTGGGCGTGCAACGCGAGGCCTCCGATGGCGAGGTCCGACGAGGCTACCACAAGGTGTCCCTGCAGGT
ACACCTGGACCGGGTGGGCAAGGGCGACAAGAAGGACGCCACCCGCTGCTTCCAGATCCTGGAAAAAGTCTATTCCATTC
TCGGTGACAGAGAACAGAGAGCAGTGTATGATGAGCAGGGAACGGTGGACGAGGACTCTCCTGTGCTCATCCAAGATCAA
GACTGGGAGGCGTATTGGCGGCTACTCTTTAAAAAGATATCTTTAGAGGACATTCAAGTTTTTGAAAAGACATACAAAGG
TTTGGAAGAAGAGCTGGCTGATATTAAGCAGGCCTATCTGGACTTCAAGGGTGACATGGATCATCAGATCATGGAGTCTG
TGCTTTGCGTGCAGTACACAGAGGAACCCAGGATAAGGATTATCATTCAGCAAGCTATTGACGCCGGAGAGGTCCCATCC
TACAATGCCTTTGTCAAAGAATCGACACAAAAGATGAATGCAAAGAAAAGGAGGGCTCAGGAAGAGGCCAAAGAAGCAGA
AATGAGCAGAAAGGAGTTGGGGCTTGATAAAGGCGTGGGTAGCCTGAAGGCAGCCATTCAGAGCAGACAAAAGGATTGGC
AAAAGGAAATGGACAATTTTCTGGCTCAGATGGAAGCAAAGTACTGCAAATCTTCCAAAGGAGGAGGGAAAAAATCTGCT
CTCAAGAAAAAAAAGAAA

Alignment

ORF - retro_ptro_1414 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.43 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYRVLGVRREASDGEVRRGYHKVSLQVHPDRVGEGDKEDATRRFQILGKVYSVLSDGEQRAVYDEQGTVD
          LY.VLGV.REASDGEVRRGYHKVSLQVH.DRVG.GDK.DATR.FQIL.KVYS.L.D.EQRAVYDEQGTVD
Retrocopy LYWVLGVQREASDGEVRRGYHKVSLQVHLDRVGKGDKKDATRCFQILEKVYSILGDREQRAVYDEQGTVD

Parental  EDSTVLTQDRDWEAYWRLLFKKISLEDIQAFEKTYKGSEEELADIKQAYLDFRGDMD-QIMESVLCVQYT
          EDS.VL.QD.DWEAYWRLLFKKISLEDIQ.FEKTYKG.EEELADIKQAYLDF.GDMD.QIMESVLCVQYT
Retrocopy EDSPVLIQDQDWEAYWRLLFKKISLEDIQVFEKTYKGLEEELADIKQAYLDFKGDMDHQIMESVLCVQYT

Parental  EEPRIRNIIQQAIDAGEVPSYNAFVKESKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQ
          EEPRIR.IIQQAIDAGEVPSYNAFVKES.QKMNA.KRRAQEEAKEAEMSRKELGLD.GV.SLKAAIQSRQ
Retrocopy EEPRIRIIIQQAIDAGEVPSYNAFVKESTQKMNAKKRRAQEEAKEAEMSRKELGLDKGVGSLKAAIQSRQ

Parental  KDRQKEMDNFLAQMEAKYCKSSKGGGKKSALKKEKK
          KD.QKEMDNFLAQMEAKYCKSSKGGGKKSALK...K
Retrocopy KDWQKEMDNFLAQMEAKYCKSSKGGGKKSALKXXXK

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	0.02 RPM	15.68 RPM
SRP007412_cerebellum	0.00 RPM	22.05 RPM
SRP007412_heart	0.03 RPM	8.28 RPM
SRP007412_kidney	0.05 RPM	14.96 RPM
SRP007412_liver	0.03 RPM	15.97 RPM
SRP007412_testis	0.11 RPM	37.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1414 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1414 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2448
Pongo abelii	retro_pabe_1799

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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,