RetrogeneDB ID: retro_hsap_2469

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:31635325..31636000(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSG00000130021
• Aliases: HDHD1, DXF68S1E, FAM16AX, GS1, HDHD1A
• Description: haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]

Sequence

>retro_hsap_2469
ATGGCTGTACCCCTGCGGCCCACCACCCACCTCCTCTTCGACGTGGATGGCCTGCTTCTGGACACTGAAAGGCTCTGTTC
AGTGGTGTTTCAAGACATATGTGATCGCTATGAAAAGGAATACACCGGGGATGTGAAGTCCCTGGTCATGGGTAAGAAGG
CGTTGGAGGTGGCGCAGGTGGTCGTGGATGTCCTGCAGCTCCTGGTGGAAGAGCTGTTGGAAGAAAGCCAAGCCAGGCCA
AGGGATGTGTTCCCCACTGCAGCGCTCATGCCAGGGGGCTGAGAAACTCATCCTCCACCTTCGGAAACACAACATCCCCT
TTGCCGTGGCCACCAGCTCAAAGTCTGCATCCTTCGAGGTGAAGACAAGCAGGCACAAGAACTCTTCAGTCTTCCATCAC
ATCATGCTGGGAGACGACCCGAAGTGAAGAGCAGCAAGCCCGACCCTGCCATATTCCTGACTTGTGCCAGGAGGTTCTCT
CTTCCTCCTCCTGTGGAGGAGTGCCCTGTCTTTGAAGATGTGCCCAACAAGGTGGAGGCAGCCCTGGACGCCAGGATGCA
GGTGGTCATGGTTCCAGATGGAAACTTGAGCCAAGACCTGACCAGAAAGGCCTCCCCGTTGCTGAGTTCCCTGCAGGACT
TCCAGCCCCAGCTGTTTGGTTTGCCCCACTACGAG

Alignment

ORF - retro_hsap_2469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPPQPVTHLIFDMDGLLLDTERLYSVVFQEICNRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQLPMS
          MA.P..P.THL.FD.DGLLLDTERL.SVVFQ.IC.RY.K.Y..DVKSLVMGKKALE.AQ...DVLQL...
Retrocopy MAVPLRPTTHLLFDVDGLLLDTERLCSVVFQDICDRYEKEYTGDVKSLVMGKKALEVAQVVVDVLQLLV-

Parental  KEELVEESQTKLKEVFPTAALMPG-AEKLIIHLRKHGIPFALATSSGSASFDMKTSRHKEFFSLFSHIVL
          .EEL.EESQ.....VFPTAALMPG.AEKLI.HLRKH.IPFA.ATSS.SASF..KTSRHK...S.F.HI.L
Retrocopy -EELLEESQARPRDVFPTAALMPG>AEKLILHLRKHNIPFAVATSSKSASFEVKTSRHKNS-SVFHHIML

Parental  GDDP-EVQHGKPDPDIFLACAKRFSPPPAMEKCLVFEDAPNGVEAALAAGMQVVMVPDGNLSRDLTTKAT
          GDDP.EV...KPDP.IFL.CA.RFS.PP..E.C.VFED.PN.VEAAL.A.MQVVMVPDGNLS.DLT.KA.
Retrocopy GDDP<EVKSSKPDPAIFLTCARRFSLPPPVEECPVFEDVPNKVEAALDARMQVVMVPDGNLSQDLTRKAS

Parental  LVLNSLQDFQPELFGLPSYE
          ..L.SLQDFQP.LFGLP.YE
Retrocopy PLLSSLQDFQPQLFGLPHYE

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	12.70 RPM
bodymap2_adrenal	0.00 RPM	11.18 RPM
bodymap2_brain	0.00 RPM	6.73 RPM
bodymap2_breast	0.00 RPM	11.09 RPM
bodymap2_colon	0.00 RPM	15.72 RPM
bodymap2_heart	0.00 RPM	14.38 RPM
bodymap2_kidney	0.00 RPM	22.73 RPM
bodymap2_liver	0.00 RPM	6.55 RPM
bodymap2_lung	0.00 RPM	9.07 RPM
bodymap2_lymph_node	0.00 RPM	19.44 RPM
bodymap2_ovary	0.00 RPM	20.82 RPM
bodymap2_prostate	0.00 RPM	10.43 RPM
bodymap2_skeletal_muscle	0.00 RPM	28.88 RPM
bodymap2_testis	0.00 RPM	12.05 RPM
bodymap2_thyroid	0.00 RPM	17.16 RPM
bodymap2_white_blood_cells	0.00 RPM	18.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2469 was not detected

EST

No EST(s) were mapped for retro_hsap_2469 retrocopy.

TSS

No TSS is located nearby retro_hsap_2469 retrocopy 5' end.

Lab

retro_hsap_2469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2469 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1537
Pongo abelii	retro_pabe_1837

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136, retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469 , retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374, retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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