RetrogeneDB ID: retro_hsap_1358

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:68265720..68266323(+)
• Located in intron of: ENSG00000072121

Retrocopy information

• Ensembl ID: ENSG00000258759
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSG00000213551
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 9 [Source:HGNC Symbol;Acc:19123]

Sequence

>retro_hsap_1358
CAGATCCTGGGAAAAGTCTATTCCGTTCCCAGTGACAAAGAACAGAGAGCAGTGTACGATGAGCAGGGAACAGTGGACGA
GGACTCTCCAGTGCTCACCCAAGACCTAGACTAGGAGGCGTACTGGCGGCTACTCTTTAAAAAGATATCTTTAGAGGACA
TTCAAGCTTTTGAAAAGACATACAAAGGTTCAGAAGAAGAGCTGGCTGATATTAAACAGGCCTATCTGGACTTCAAGGGT
GACATGGATCAGATCATGGAGTCTGTGCTTTGCGTGCAGTACACAGAGGAACCCAGGATAAGGAATATTGTTCAGCAAGC
TATTGACGCCAGAGCGGTGCAATCCTATAAGGCCTTTGTCAAAGAATCGAAACAAAAGATGAATGCAAGGAAAAGGAGGG
CTCAGGAAGAGGCCAAAGAAGCAGAAACGAGCAGAAAGGAGTTGGGGCTTGATGAAGGCGTGGATAGCCTGAAGGCAGCC
ATTCAGAGCAGACAAAAGGATCGGCAAAAGGAAATGGACAGTTTTCTGGCTCAGATGGAAGCAAAGTACTGCAAGTCTTC
CAAAGGAGGAGGGAAAAAATCTGCTCTCAAGAAATAAAAGAAA

Alignment

ORF - retro_hsap_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.03 %
• Parental protein coverage: 77.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QILGKVYSVLSDREQRAVYDEQGTVDEDSPVLTQDRDWEAYWRLLFKKISLEDIQAFEKTYKGSEEELAD
          QILGKVYSV.SD.EQRAVYDEQGTVDEDSPVLTQD.D.EAYWRLLFKKISLEDIQAFEKTYKGSEEELAD
Retrocopy QILGKVYSVPSDKEQRAVYDEQGTVDEDSPVLTQDLD*EAYWRLLFKKISLEDIQAFEKTYKGSEEELAD

Parental  IKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEVPSYNAFVKESKQKMNARKRRAQEEAKE
          IKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNI.QQAIDA..V.SY.AFVKESKQKMNARKRRAQEEAKE
Retrocopy IKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIVQQAIDARAVQSYKAFVKESKQKMNARKRRAQEEAKE

Parental  AEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEAKYCKSSKGGGKKSALKKEKK
          AE.SRKELGLDEGVDSLKAAIQSRQKDRQKEMD.FLAQMEAKYCKSSKGGGKKSALKK.KK
Retrocopy AETSRKELGLDEGVDSLKAAIQSRQKDRQKEMDSFLAQMEAKYCKSSKGGGKKSALKK*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
bodymap2_adipose	0.00 RPM	4.45 RPM
bodymap2_adrenal	0.02 RPM	9.66 RPM
bodymap2_brain	0.00 RPM	10.43 RPM
bodymap2_breast	0.00 RPM	5.62 RPM
bodymap2_colon	0.00 RPM	6.15 RPM
bodymap2_heart	0.00 RPM	3.69 RPM
bodymap2_kidney	0.00 RPM	8.79 RPM
bodymap2_liver	0.00 RPM	3.11 RPM
bodymap2_lung	0.00 RPM	3.60 RPM
bodymap2_lymph_node	0.00 RPM	17.12 RPM
bodymap2_ovary	0.04 RPM	13.65 RPM
bodymap2_prostate	0.00 RPM	6.60 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.13 RPM
bodymap2_testis	0.00 RPM	11.95 RPM
bodymap2_thyroid	0.00 RPM	7.53 RPM
bodymap2_white_blood_cells	0.00 RPM	6.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1358 was not detected

EST

No EST(s) were mapped for retro_hsap_1358 retrocopy.

TSS

No TSS is located nearby retro_hsap_1358 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CTGAGGTTACAGTGAGAAGAATAAGAG (27 nt long)
• Reverse primer: CTGGCGTCAATAGCTTGCTGAAC (23 nt long)
• Anneling temperature: 60 °C
• (Expected) product size: 580
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1358 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_931
Gorilla gorilla	retro_ggor_1058
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).