RetrogeneDB ID: retro_hsap_1583

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:66063512..66064082(-)
• Located in intron of: ENSG00000174485

Retrocopy information

• Ensembl ID: ENSG00000259924
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJB14
• Ensembl ID: ENSG00000164031
• Aliases: DNAJB14, EGNR9427, PRO34683
• Description: DnaJ (Hsp40) homolog, subfamily B, member 14 [Source:HGNC Symbol;Acc:25881]

Sequence

>retro_hsap_1583
AGGTTTTGTGAAGTTGATATAACTCCAGAAGACTTGTTTAATATATTTTTTGGGGGTGGATTTCCTTCAGGTAGTATACA
TTCTTTTTCAAATGGAAGAGCTGGTTATAGCCAACAACATCAGCATTGACATAGTGGACATGAAAGAGAAGAGGAAAGAG
GAGATGGAGGTTTTTCTGTGTTTATCCAGCTGATGCCCATAATTGTATTGATCCTCGTGTCATTATTAAGCCAGTTGATG
GTCTGTAATCCTCCTTATTCCTTCTATCCCAGATCTGGAACAGGGCAAACTATTAAAACGCAGACAGAAAACTTGGGTGG
TGTTTATTATGTCAGCAAGGACTTTAAAAATGAATATAAAGGAATGTTATTACAAAAGGCAGAAAAGAGTGTGGAGGAAG
ATTATGTGACTAATATTCGAAATAACTGCTGGAAAGAAAGACAACAAAAAACAGATATGCAGTATGCAGCAAAAGTATAC
CGTGGTGATCGACTCCGAAGGAAGTCAGATGCCTTGAGCATGGACAACTGTAAAGAATTAGAGCGGCTTACCGGTCTTTA
TAAAGGAGGA

Alignment

ORF - retro_hsap_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 50.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGCEADITPEDLFNIFFGGGFPSGSVHSFSNGRAGYSQQHQHRHSGHEREEERGDGGFSVFIQLMPIIVL
          R.CE.DITPEDLFNIFFGGGFPSGS.HSFSNGRAGYSQQHQH.HSGHEREEERGDGGFSVFIQLMPIIVL
Retrocopy RFCEVDITPEDLFNIFFGGGFPSGSIHSFSNGRAGYSQQHQH*HSGHEREEERGDGGFSVFIQLMPIIVL

Parental  ILVSLLSQLMVSNPPYSLYPRSGTGQTIKMQTENLGVVYYVNKDFKNEYKGMLLQKVEKSVEEDYVTNIR
          ILVSLLSQLMV.NPPYS.YPRSGTGQTIK.QTENLG.VYYV.KDFKNEYKGMLLQK.EKSVEEDYVTNIR
Retrocopy ILVSLLSQLMVCNPPYSFYPRSGTGQTIKTQTENLGGVYYVSKDFKNEYKGMLLQKAEKSVEEDYVTNIR

Parental  NNCWKERQQKTDMQYAAKVYRDDRLRRKADALSMDNCKELERLTSLYKGG
          NNCWKERQQKTDMQYAAKVYR.DRLRRK.DALSMDNCKELERLT.LYKGG
Retrocopy NNCWKERQQKTDMQYAAKVYRGDRLRRKSDALSMDNCKELERLTGLYKGG

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	0.14 RPM	61.64 RPM
bodymap2_adrenal	0.92 RPM	58.07 RPM
bodymap2_brain	0.40 RPM	136.87 RPM
bodymap2_breast	0.53 RPM	61.60 RPM
bodymap2_colon	0.08 RPM	66.77 RPM
bodymap2_heart	0.04 RPM	31.85 RPM
bodymap2_kidney	0.15 RPM	83.59 RPM
bodymap2_liver	0.09 RPM	21.44 RPM
bodymap2_lung	0.21 RPM	64.45 RPM
bodymap2_lymph_node	0.11 RPM	74.98 RPM
bodymap2_ovary	0.21 RPM	70.44 RPM
bodymap2_prostate	0.00 RPM	76.24 RPM
bodymap2_skeletal_muscle	0.27 RPM	17.35 RPM
bodymap2_testis	0.25 RPM	52.11 RPM
bodymap2_thyroid	0.04 RPM	73.93 RPM
bodymap2_white_blood_cells	0.00 RPM	87.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1583 was not detected

EST

No EST(s) were mapped for retro_hsap_1583 retrocopy.

TSS

No TSS is located nearby retro_hsap_1583 retrocopy 5' end.

Lab

retro_hsap_1583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1583 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1066
Pongo abelii	retro_pabe_1304

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583 ,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.15 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.18 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.19 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.15 RPM
GBR_HG00114	0.16 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.26 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.36 RPM
GBR_HG00142	0.39 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.26 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.24 RPM

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Indel association:

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