RetrogeneDB ID: retro_hsap_3557

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:10460144..10460774(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000238076
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL48
• Ensembl ID: ENSG00000175581
• Aliases: None
• Description: mitochondrial ribosomal protein L48 [Source:HGNC Symbol;Acc:16653]

Sequence

>retro_hsap_3557
ATGAGCAGAACCTTGGAAAAAGTGCTGTGCCTGAGGAACAATACCACTTTTAAGCAAGGCTTTTCACTCTTAAGGCTTAG
AACTTCAGCAGAGAAGCCCATCTATTCTGTAGGTGGCATTCTACTAAGTACTAGTCGGCCCTACAAGACAAAGCCCACCC
ACGCCATTGGAAAGTACAAGCACCTAATTAAAGCAGAAGAGCCCGAGAAGAAGCAAAAAGTGGAAGTGAAACTCATTAAT
TTGGGGACAGATGATGAATATGGGGTTTTAAACATTCACCTGCCTGCATATGACATGACCCTGGCAGAGAGTTATGCCCA
GTATGTTCACAACTTCTGCAACTCTCTCTCCATTAAAGTCGAGGAAAGTTATGTGATGCCAACCAAAACCACTGAAGTGT
TGTGGTTGCAGGACCAAGGCAGCAAAACGTTCCTGGACTCAGTGCTTACCACCCATGAGCGAGTGGTTCACATCAGCAGT
TTGAGTGCTACGTTTGCAGAGATTTTCTTGGAAATAATCCAAAGCAGTCTTCCTGAAGGAGTCAGATTGTCGTTGAAGGA
GCACACTGAAGAAGACTTCAAGGGAAGATTCAAAGCTCGACCAGAACTGGAAGAACGGTTGGCCAAGTTG

Alignment

ORF - retro_hsap_3557 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.63 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGTLEKVLCLRNNTIFKQAFSLLRFRTSGEKPIYSVGGILLSISRPYKTKPTHGIGKYKHLIKAEEPKK
          MS.TLEKVLCLRNNT.FKQ.FSLLR.RTS.EKPIYSVGGILLS.SRPYKTKPTH.IGKYKHLIKAEEP.K
Retrocopy MSRTLEKVLCLRNNTTFKQGFSLLRLRTSAEKPIYSVGGILLSTSRPYKTKPTHAIGKYKHLIKAEEPEK

Parental  KKGKVEVRAINLGTDYEYGVLNIHLTAYDMTLAESYAQYVHNLCNSLSIKVEESYAMPTKTIEVLQLQDQ
          K..KVEV..INLGTD.EYGVLNIHL.AYDMTLAESYAQYVHN.CNSLSIKVEESY.MPTKT.EVL.LQDQ
Retrocopy KQ-KVEVKLINLGTDDEYGVLNIHLPAYDMTLAESYAQYVHNFCNSLSIKVEESYVMPTKTTEVLWLQDQ

Parental  GSKMLLDSVLTTHERVVQISGLSATFAEIFLEIIQSSLPEGVRLSVKEHTEEDFKGRFKARPELEELLAK
          GSK..LDSVLTTHERVV.IS.LSATFAEIFLEIIQSSLPEGVRLS.KEHTEEDFKGRFKARPELEE.LAK
Retrocopy GSKTFLDSVLTTHERVVHISSLSATFAEIFLEIIQSSLPEGVRLSLKEHTEEDFKGRFKARPELEERLAK

Parental  L
          L
Retrocopy L

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	9.26 RPM
bodymap2_adrenal	0.00 RPM	22.23 RPM
bodymap2_brain	0.00 RPM	23.28 RPM
bodymap2_breast	0.00 RPM	12.41 RPM
bodymap2_colon	0.00 RPM	18.62 RPM
bodymap2_heart	0.00 RPM	13.02 RPM
bodymap2_kidney	0.00 RPM	20.83 RPM
bodymap2_liver	0.00 RPM	13.08 RPM
bodymap2_lung	0.00 RPM	9.34 RPM
bodymap2_lymph_node	0.00 RPM	13.47 RPM
bodymap2_ovary	0.00 RPM	19.89 RPM
bodymap2_prostate	0.00 RPM	22.85 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.73 RPM
bodymap2_testis	0.00 RPM	10.63 RPM
bodymap2_thyroid	0.00 RPM	17.42 RPM
bodymap2_white_blood_cells	0.00 RPM	20.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3557 was not detected

EST

No EST(s) were mapped for retro_hsap_3557 retrocopy.

TSS

No TSS is located nearby retro_hsap_3557 retrocopy 5' end.

Lab

retro_hsap_3557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3557 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2417

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557 ,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 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	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 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	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 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	0.00 RPM

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Indel association:

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