RetrogeneDB ID: retro_hsap_290

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:202765603..202766222(+)
• Located in intron of: ENSG00000117139

Retrocopy information

• Ensembl ID: ENSG00000226148
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSG00000013306
• Aliases: SLC25A39, CGI69
• Description: solute carrier family 25, member 39 [Source:HGNC Symbol;Acc:24279]

Sequence

>retro_hsap_290
CTGAGCCCTTACCTCTACATAACCTTGGTAGCTGGTGTGCTGGTCCACCCTGGCACTATCACTGCAATCATCAGTGCCCT
GGAGCTTATGCAGACAAAGCTGCAGGTTTAGCATATGTTATACTATGTGCTGGTACCTGTGTTTGAGCTCCGGTGGCTTA
GAGTGGTTGGTGCTCACTGTGGCTGTGCCGGGGCCCCACTCTCCTTAGAAATGTGCCCTTCTCAGCCCTGTACTGGTTCA
ACTACGAGCTAGTGAAGAGCTGGCTGAATGGGCTCAGGCCAAAGGAACTCCATGGTCCCATGACAACCATAGGAGTCAGC
TTTGCAGCTGGCAGCATCACCATGATGCTGGCTACAGTGCTGACCCTAACCTTTGTCGTGATGAAGACTCAACACCAGGC
CACACTCGGAGTGATGGAAGCCGTGGAAGTGACATCCCTGGATGCGGACTCTACCTGGTTGCTCAGAGGTGGATCTGTGC
CAAGTCGGGCATCAGAGGGCTCTTTGCAGGCTTCCTCCCTTGGATCATCAAGTCTATCCCCTCCTATGCTATCACGATCA
CCACTTATGAGTTCAGCAAAAGTCTCTTAAAGAGACTCAATCAGGACCAGCATCTGGGC

Alignment

ORF - retro_hsap_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.24 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSDLYAPMVAGALARLGTVT-VISPLELMRTKLQAQHVSYREL-GACVRTAVAQGGWRSLWLGWGPTAL
          L...LY...VAG.L...GT.T..IS.LELM.TKLQ..H..Y..L.G.CV...VA..GW.SLWL..GPT.L
Retrocopy LSPYLYITLVAGVLVHPGTITAIISALELMQTKLQV*HMLYYVL<GTCV*APVA*SGWCSLWLCRGPTLL

Parental  RDVPFSALYWFNYELVKSWLNGFRPKD----QTSVGMSFVAGGISGTVAAVLTLPFDVVKTQRQVALGAM
          R.VPFSALYWFNYELVKSWLNG.RPK......T..G.SF.AG.I....A.VLTL.F.V.KTQ.Q..LG.M
Retrocopy RNVPFSALYWFNYELVKSWLNGLRPKELHGPMTTIGVSFAAGSITMMLATVLTLTFVVMKTQHQATLGVM

Parental  EAVRVNPLHVDSTWLL-LRRIRAESGTKGLFAGFLPRIIKAAPSCAIMISTYEFGKSFFQRLNQDRLLG
          EAV.V..L..DSTWLL..R.I.A.SG..GLFAGFLP.IIK..PS.AI.I.TYEF.KS...RLNQD..LG
Retrocopy EAVEVTSLDADSTWLL<QRWICAKSGIRGLFAGFLPWIIKSIPSYAITITTYEFSKSLLKRLNQDQHLG

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	26.89 RPM
bodymap2_adrenal	0.00 RPM	48.70 RPM
bodymap2_brain	0.00 RPM	10.45 RPM
bodymap2_breast	0.00 RPM	33.44 RPM
bodymap2_colon	0.00 RPM	40.45 RPM
bodymap2_heart	0.04 RPM	13.22 RPM
bodymap2_kidney	0.00 RPM	78.19 RPM
bodymap2_liver	0.00 RPM	47.82 RPM
bodymap2_lung	0.00 RPM	70.04 RPM
bodymap2_lymph_node	0.00 RPM	55.55 RPM
bodymap2_ovary	0.00 RPM	43.82 RPM
bodymap2_prostate	0.00 RPM	35.94 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.68 RPM
bodymap2_testis	0.04 RPM	58.46 RPM
bodymap2_thyroid	0.00 RPM	60.09 RPM
bodymap2_white_blood_cells	0.00 RPM	24.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_290 was not detected

EST

No EST(s) were mapped for retro_hsap_290 retrocopy.

TSS

No TSS is located nearby retro_hsap_290 retrocopy 5' end.

Lab

retro_hsap_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_290 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_239

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290 ,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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