RetrogeneDB ID: retro_ggor_1058

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:48911824..48912439(+)
• Located in intron of: ENSGGOG00000015342

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSGGOG00000015046
• Aliases: None
• Description: None

Sequence

>retro_ggor_1058
ACTCTCTGCCCTCAGATCCTGGGAAAAGTCTATTCCGTCCTCAGTGACAAAGAACAGAGAGCAGTGTACGATGAGCAGGG
AACAGTGGACGAGGACTCTCCAGTGCTCACCCAAGACCTAGACTAGGAGGCGTACTGGCGGCTACTCTTTAAAAAGATAT
CTTTAGAGGACATTCAAGCTTTTGAAAAGACATACAAAGGTTCAGAAGAAGAGCTGGCTGATATTAAACAGGCCTATCTG
GACTTCAAGGGTGACATGGATCAGATCATGGAGTCTGTGCTTTGCGTGCAGTACACAGAGGAACCCAGGATAAGGAATAT
CGTTCAGCAAGCTATTAACGCCAGAGCAGTGCAATCCTATAAGGCCTTTGTCAAAGAATCGAAACAAAAGATGAATGCAA
GGAAAAGGAGGGCTCAGGAAGAGGCCAAAGAAGCAGAAACGAGCAGAAAGGAGTTGGGGCTTGATGAAGGCGTGGATAGC
CTGAAGGCAGCCATTCACAGCAGACAAAAGGATCGGCAAAAGGAAATGGACAGTTTTCTGGCTCAGATGGAAGCAAAGTA
CTGCAAGTCTTCCAAAGGAGGAGGGAAAAAATCTGCTCTCAAGAAATAGAAGAAA

Alignment

ORF - retro_ggor_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.2 %
• Parental protein coverage: 78.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TRCFQILGKVYSVLSDREQRAVYDEQGTVDEDSPVLTQDRDWEAYWRLLFKKISLEDIQAFEKTYKGSEE
          T.C.QILGKVYSVLSD.EQRAVYDEQGTVDEDSPVLTQD.D.EAYWRLLFKKISLEDIQAFEKTYKGSEE
Retrocopy TLCPQILGKVYSVLSDKEQRAVYDEQGTVDEDSPVLTQDLD*EAYWRLLFKKISLEDIQAFEKTYKGSEE

Parental  ELADIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKESKQKMNARKRRAQE
          ELADIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNI.QQAI.A..V.SY.AFVKESKQKMNARKRRAQE
Retrocopy ELADIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIVQQAINARAVQSYKAFVKESKQKMNARKRRAQE

Parental  EAKEAEMSRKELGLDESVDSLKAAIQSRQKDRQKEMDNFLAQMEAKYCKSSKGGGKKSALKKEKK
          EAKEAE.SRKELGLDE.VDSLKAAI.SRQKDRQKEMD.FLAQMEAKYCKSSKGGGKKSALKK.KK
Retrocopy EAKEAETSRKELGLDEGVDSLKAAIHSRQKDRQKEMDSFLAQMEAKYCKSSKGGGKKSALKK*KK

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	10.69 RPM
SRP007412_cerebellum	0.00 RPM	13.99 RPM
SRP007412_heart	0.00 RPM	2.44 RPM
SRP007412_kidney	0.04 RPM	5.93 RPM
SRP007412_liver	0.00 RPM	4.17 RPM
SRP007412_testis	0.00 RPM	27.35 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1058 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1358
Pan troglodytes	retro_ptro_931
Pongo abelii	retro_pabe_1126

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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,