RetrogeneDB ID: retro_hsap_836

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:303856..304319(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000255533
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSG00000062582
• Aliases: MRPS24, MRP-S24, S24mt, bMRP-47, bMRP47
• Description: mitochondrial ribosomal protein S24 [Source:HGNC Symbol;Acc:14510]

Sequence

>retro_hsap_836
CGGGTGCCGTCCCGGGGCCGAGAGCTGCCTTGCGCGGGGCGGGCCCCGCACACCTCCGCGGTCTGTAACAAGAACCGGCG
GCCCGAGTCCGCCGAGGCCAGGGGGACAAGCCGGTGACCTATGAGGACGCACACGCGCCGCACTTCGTCGCCCGCCGTGA
GGGCCAGAGGTCGCTCACGCGGGGAACCCTGGTGGGGAGGACCATGCGGCGGAGCGAACGGTGGAGGATGCTTTCCGTCG
CAAGTTCATGTGGGGTGCCTTCCCGGGCTGCCTGGCTGACCCGCTGGTTTTACAGTGCTGGGCCAACCGGTTGGAGATCT
GTGCCCTGGTCCCGAGGCACTTGCCTGCCCGCAAGTTCTACTTCCTCGTGGGCTACAGTGAAACTTTGCTGTCCCACTTT
TACAAATGTCCTCTGCCACTCCACCTCCAAACTGTGCCCTCAAAGGTTGTGTATAAGGACCTG

Alignment

ORF - retro_hsap_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.25 %
• Parental protein coverage: 92.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVLSWSRELPCAWRALHTSPVCAKNR-AARVRVSKGDKPVTYEEAHAPHYIAHRKGWLSL-HTGNLDGED
          RV.S..RELPCA.RA.HTS.VC.KNR.AARVR...GDKPVTYE.AHAPH..A.R.G..SL.H.GN..GED
Retrocopy RVPSRGRELPCAGRAPHTSAVCNKNR<AARVRRGQGDKPVTYEDAHAPHFVARREGQRSL<HAGNPGGED

Parental  HAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEICAVVLRQLSPHKYYFLVGYSETLLSYFYKCP
          HAAERTVED.F.RKFMWG.FPGCLAD.LVL....N.LEICA.V.R.L...K.YFLVGYSETLLS.FYKCP
Retrocopy HAAERTVEDAFRRKFMWGAFPGCLADPLVLQCWANRLEICALVPRHLPARKFYFLVGYSETLLSHFYKCP

Parental  VRLHLQTVPSKVVYKYL
          ..LHLQTVPSKVVYK.L
Retrocopy LPLHLQTVPSKVVYKDL

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	0.44 RPM
bodymap2_adrenal	0.08 RPM	0.49 RPM
bodymap2_brain	0.00 RPM	0.19 RPM
bodymap2_breast	0.00 RPM	0.31 RPM
bodymap2_colon	0.00 RPM	0.46 RPM
bodymap2_heart	0.00 RPM	0.44 RPM
bodymap2_kidney	0.00 RPM	0.56 RPM
bodymap2_liver	0.00 RPM	0.09 RPM
bodymap2_lung	0.00 RPM	0.44 RPM
bodymap2_lymph_node	0.02 RPM	0.29 RPM
bodymap2_ovary	0.00 RPM	0.25 RPM
bodymap2_prostate	0.00 RPM	0.31 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.13 RPM
bodymap2_testis	0.26 RPM	0.25 RPM
bodymap2_thyroid	0.02 RPM	0.41 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_836 was not detected

EST

No EST(s) were mapped for retro_hsap_836 retrocopy.

TSS

No TSS is located nearby retro_hsap_836 retrocopy 5' end.

Lab

retro_hsap_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_836 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836 ,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,

Population studies

Expression level across human populations :

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