RetrogeneDB ID: retro_hsap_2954

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:84398676..84399568(+)
• Located in intron of: ENSG00000163322

Retrocopy information

• Ensembl ID: ENSG00000213608
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSG00000102078
• Aliases: SLC25A14, BMCP1, UCP5
• Description: solute carrier family 25 (mitochondrial carrier, brain), member 14 [Source:HGNC Symbol;Acc:10984]

Sequence

>retro_hsap_2954
CAGCAAAGTACCACTGTAAGCCATGAGATGTCTCGTCTGAACTGGAAACCCTTTGTATATGACGCCTTGCCTCTATCACT
GCTGAGTTTGGAACTTTCCCCATGGACCTTGCCAAAACACGACTTCAGGTAGGTTCAAGGCCAAAGCATTGATGTCCGTT
TCAAAGAAACAAAATATAGACGGATGTTTCATGCTTTGTTTTGGATCTATAAAGCGGAAGGTGTATTGGCTCTGTATTCA
GGAATTGCTCCTGTTTTGCAAAGACAAGCATCATATGGCACCATTAAAATTGGGATTTACCAAAGCTTGAAGCAATTATC
TGTAGAACGTTTAGAAGATGAAACTCTTTTAATCAACATGATCTGTGGGGTAGTGTCAGGGGTGATATTTTCCACTATAG
CCAATCCCACCGATGTTCTAAAGATTCGAATGCAGGCTCAAGGAAGTTTGTTCCAAGGGAGCATGATTGGCAGCTTCATC
GATATATACCAACAGGAAGGCACCAGGGGTCTGTGGAGGAGTGTGGTTCCAACTGCTCAGCATGCTGCCATCGTTGTGGG
AGTAGAGCTACCAGTCTATGATTTTACTAAGAAGCACTTAATATTGTCAGGAATGATGGAAGACACAACTTTAACTCACT
TTGTTTCCAGCTTTACATATGGTTTGGCTGGGGCTCTTGCCTCTAATCCAGGTGATGTGGCAGGCACTCACGTGATGAAC
CAGAGGGCAATCGTGGGACATGTGGATCTCTATAAGGGCACTTTGGATGGTATTTTAAAAATGTGGAAACATGAGGGCTT
TTTTGTATTCTAAAGGATTTTGGCCAAACTGGCTTTGGCGTGGACCCTGGAACATCATTCTTTAAATTACATATGAGTAG
CTCAAGAGGCTT

Alignment

ORF - retro_hsap_2954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.77 %
• Parental protein coverage: 92.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QKSTTVSHEMSGLNWKPFVYGGL-ASIVAEFGTF-PVDLTKTRLQ-VQGQSIDARFKEIKYRGMFHALFR
          Q.STTVSHEMS.LNWKPFVY..L.ASI.AEFGTF.P..L.K.....VQGQSID.RFKE.KYR.MFHALF.
Retrocopy QQSTTVSHEMSRLNWKPFVYDAL<ASITAEFGTF>PWTLPKHDFR*VQGQSIDVRFKETKYRRMFHALFW

Parental  ICKEEGVLALYSGIAPALLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMICGVVSGVISSTIANPTD
          I.K.EGVLALYSGIAP.L.RQASYGTIKIGIYQSLK.L.VERLEDETLLINMICGVVSGVI.STIANPTD
Retrocopy IYKAEGVLALYSGIAPVLQRQASYGTIKIGIYQSLKQLSVERLEDETLLINMICGVVSGVIFSTIANPTD

Parental  VLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRGVVPTAQRAAIVVGVELPVYDITKKHLILSGMMGD
          VLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWR.VVPTAQ.AAIVVGVELPVYD.TKKHLILSGMM.D
Retrocopy VLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRSVVPTAQHAAIVVGVELPVYDFTKKHLILSGMMED

Parental  TILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRAIVGHVDLYKGTVDGILKMWKHEGF-FALYKGF-WP
          T.LTHFVSSFT.GLAGALASNP.DV..T..MNQRAIVGHVDLYKGT.DGILKMWKHEGF.F...K.F.WP
Retrocopy TTLTHFVSSFTYGLAGALASNPGDVAGTHVMNQRAIVGHVDLYKGTLDGILKMWKHEGF<FCILKDF<WP

Parental  NWLRLGPWNIIFFITYEQLKRL
          NWL..GPWNII..ITYE.LKRL
Retrocopy NWLWRGPWNIIL*ITYE*LKRL

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	2.27 RPM
bodymap2_adrenal	0.00 RPM	7.31 RPM
bodymap2_brain	0.07 RPM	15.21 RPM
bodymap2_breast	0.00 RPM	4.61 RPM
bodymap2_colon	0.00 RPM	5.28 RPM
bodymap2_heart	0.00 RPM	2.79 RPM
bodymap2_kidney	0.06 RPM	7.94 RPM
bodymap2_liver	0.00 RPM	3.27 RPM
bodymap2_lung	0.00 RPM	4.78 RPM
bodymap2_lymph_node	0.09 RPM	6.19 RPM
bodymap2_ovary	0.19 RPM	7.73 RPM
bodymap2_prostate	0.09 RPM	9.01 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.33 RPM
bodymap2_testis	0.08 RPM	14.89 RPM
bodymap2_thyroid	0.08 RPM	5.93 RPM
bodymap2_white_blood_cells	0.00 RPM	4.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2954 was not detected

EST

No EST(s) were mapped for retro_hsap_2954 retrocopy.

TSS

No TSS is located nearby retro_hsap_2954 retrocopy 5' end.

Lab

retro_hsap_2954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2954 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2048
Pongo abelii	retro_pabe_2450

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954 ,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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