RetrogeneDB ID: retro_hsap_938

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:124677713..124678164(-)
• Located in intron of: ENSG00000245498

Retrocopy information

• Ensembl ID: ENSG00000254941
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF181
• Ensembl ID: ENSG00000168894
• Aliases: None
• Description: ring finger protein 181 [Source:HGNC Symbol;Acc:28037]

Sequence

>retro_hsap_938
ATGACAGCCTATTTCAATGAACAGGACTGCAAGCTCTTGAACCCCAAGCAGGAGACCCTAACCCACATGCTGCTGGAGCT
CACCAGATCACTTTTCAATAGGATGGATTTTGAAGACTCGGGGATGGCAGTAAATTGGAATCACCACCTGCCTCCACCAG
CTGCCAAGACAGTGTGGTTGGGAACCTCCCCAGGACAGTCATCAGGAGCTCTCAGGCTGAGAGGCACACACAAGTGCCCC
ATGTGCTTGAGGAGGAGGAGGCTGTTGTTGGGATGCCTTGCCATTAGCTTTTCCATTCTAACTGCATTTTGCCCCGGCTA
AGCAAGACAAATCCCTGTCCCTTGTGCTGCCAGGAGCTGCCCGCTGTTAACGACACTTGTGAGGAGCACAGAGGAGATAA
GGCTCGAAACAGCAGCAGCAGCACTGTCTGGAGAACCTCTACAGAGCCATG

Alignment

ORF - retro_hsap_938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.58 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDPEQETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLP-PPAAK-TVVENLPRTVIR
          M..YF.E.DC....P.QET.T.MLLEL.RSLFNRMDFED.G..V.W.HHLP.P.A....VV.NLPRTVIR
Retrocopy MTAYFNEQDCKLLNPKQETLTHMLLELTRSLFNRMDFEDSGMAVNWNHHLPPPAAKT<SVVGNLPRTVIR

Parental  GSQAELKCPVCLLEFEEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRYELPTDDDTYEEHRRDKAR-K
          .SQAE....V.....EEEE....MPCH.LFHS.CILP.LSKTN.CPLC..ELP...DT.EEHR.DKAR.K
Retrocopy SSQAERHTQVPHV-LEEEEAVVGMPCH*LFHSNCILPRLSKTNPCPLCCQELPAVNDTCEEHRGDKAR<K

Parental  QQQQHRLENLHGAM
          QQQQH.LENL..AM
Retrocopy QQQQHCLENLYRAM

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	0.22 RPM	28.07 RPM
bodymap2_adrenal	0.31 RPM	31.36 RPM
bodymap2_brain	0.45 RPM	15.78 RPM
bodymap2_breast	0.39 RPM	26.93 RPM
bodymap2_colon	0.19 RPM	19.78 RPM
bodymap2_heart	0.33 RPM	15.03 RPM
bodymap2_kidney	0.12 RPM	29.64 RPM
bodymap2_liver	0.15 RPM	33.19 RPM
bodymap2_lung	0.14 RPM	45.85 RPM
bodymap2_lymph_node	1.10 RPM	27.12 RPM
bodymap2_ovary	0.46 RPM	18.00 RPM
bodymap2_prostate	0.81 RPM	36.48 RPM
bodymap2_skeletal_muscle	0.36 RPM	31.97 RPM
bodymap2_testis	0.49 RPM	30.09 RPM
bodymap2_thyroid	1.71 RPM	27.59 RPM
bodymap2_white_blood_cells	0.18 RPM	35.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_938 was not detected

EST

No EST(s) were mapped for retro_hsap_938 retrocopy.

TSS

No TSS is located nearby retro_hsap_938 retrocopy 5' end.

Lab

retro_hsap_938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_938 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_650
Gorilla gorilla	retro_ggor_759
Pongo abelii	retro_pabe_807
Macaca mulatta	retro_mmul_1128

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019647	3 retrocopies	retro_cjac_2423, retro_cjac_355, retro_cjac_3849,
Homo sapiens	ENSG00000070423	1 retrocopy	retro_hsap_1770,
Homo sapiens	ENSG00000168894	3 retrocopies	retro_hsap_1005, retro_hsap_3771, retro_hsap_938 ,
Macaca mulatta	ENSMMUG00000017824	3 retrocopies	retro_mmul_1128, retro_mmul_1637, retro_mmul_808,
Pongo abelii	ENSPPYG00000012225	2 retrocopies	retro_pabe_3083, retro_pabe_807,
Pan troglodytes	ENSPTRG00000012138	2 retrocopies	retro_ptro_2557, retro_ptro_650,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.34 RPM
CEU_NA11843	0.34 RPM
CEU_NA11930	0.62 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.60 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.33 RPM
CEU_NA12872	0.52 RPM
CEU_NA12873	0.57 RPM
FIN_HG00183	0.69 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.44 RPM
FIN_HG00321	1.06 RPM
FIN_HG00328	0.33 RPM
FIN_HG00338	0.38 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.27 RPM
FIN_HG00377	0.30 RPM
FIN_HG00378	0.17 RPM
GBR_HG00099	0.73 RPM
GBR_HG00111	0.69 RPM
GBR_HG00114	0.55 RPM
GBR_HG00119	0.62 RPM
GBR_HG00131	0.69 RPM
GBR_HG00133	0.39 RPM
GBR_HG00134	0.35 RPM
GBR_HG00137	0.52 RPM
GBR_HG00142	0.78 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.27 RPM
TSI_NA20518	0.28 RPM
TSI_NA20532	0.44 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	0.44 RPM
TSI_NA20771	0.28 RPM
TSI_NA20786	0.29 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.54 RPM
YRI_NA18907	0.45 RPM
YRI_NA18916	0.91 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.48 RPM
YRI_NA19114	0.94 RPM
YRI_NA19118	0.33 RPM
YRI_NA19213	0.43 RPM
YRI_NA19214	0.42 RPM
YRI_NA19223	0.64 RPM

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Indel association:

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