RetrogeneDB ID: retro_hsap_3771

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:105170655..105171115(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000223886
• 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_3771
ATGGCGTCCTATATCGATGAACACGACTGTGAGCCGTTGGACCCTCAAGCAGGAGACTCGAACCAACATGGTGCTGGAGC
TCGTAAGGTCACTTTTGAATAGGATGGACTTTGAAGACTTGGGGTTGGTAGTAGATTGGGACCACCACCTGCCTCCACCG
GCTGCCAAGATTGTGGTTGAGAACCTCTCCAGGACAGTCATCAGAGGCTCTCAAGGCTGAGCTCAAGTGCCCCGTGTATC
TTTTGGAATCTGAGGAGGAGACTGCCATTGAGATGCTTCCCAACACCTTTTTCATTCCAGTTGCATTCTGCCCTGGCTAA
GCAAGACAAATTCCTGTCCCTTGTGCCGCCATGAGCTGCCCACTGATGACTACACTTATGAGGAACACAGACGAGATAAG
GCTCGAAAACAGCAGCAGCAGCAGAACCGACTGGAGAACCTCCATGGAGCCATGTACACG

Alignment

ORF - retro_hsap_3771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDPE-QETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPRTVIRG
          MASY.DEHDCEP.DP..QETRTNM.LEL.RSL.NRMDFEDLGLVVDWDHHLPPPAAK.VVENL.RTVIRG
Retrocopy MASYIDEHDCEPLDPQ>QETRTNMVLELVRSLLNRMDFEDLGLVVDWDHHLPPPAAKIVVENLSRTVIRG

Parental  SQ-AELKCPVCLLEFEEEETAIEM-PCHHLFHSSCILPWLSKTNSCPLCRYELPTDDDTYEEHRRDKARK
          SQ.AELKCPV.LLE..EEETAIEM....HLFHSSCILPWLSKTNSCPLCR.ELPTDD.TYEEHRRDKARK
Retrocopy SQ>AELKCPVYLLE-SEEETAIEM<ASQHLFHSSCILPWLSKTNSCPLCRHELPTDDYTYEEHRRDKARK

Parental  -QQQQHRLENLHGAMYT
          .QQQQ.RLENLHGAMYT
Retrocopy QQQQQNRLENLHGAMYT

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	28.07 RPM
bodymap2_adrenal	0.00 RPM	31.36 RPM
bodymap2_brain	0.00 RPM	15.78 RPM
bodymap2_breast	0.00 RPM	26.93 RPM
bodymap2_colon	0.19 RPM	19.78 RPM
bodymap2_heart	0.00 RPM	15.03 RPM
bodymap2_kidney	0.00 RPM	29.64 RPM
bodymap2_liver	0.00 RPM	33.19 RPM
bodymap2_lung	0.07 RPM	45.85 RPM
bodymap2_lymph_node	0.16 RPM	27.12 RPM
bodymap2_ovary	0.39 RPM	18.00 RPM
bodymap2_prostate	0.00 RPM	36.48 RPM
bodymap2_skeletal_muscle	0.09 RPM	31.97 RPM
bodymap2_testis	0.15 RPM	30.09 RPM
bodymap2_thyroid	0.09 RPM	27.59 RPM
bodymap2_white_blood_cells	0.16 RPM	35.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3771 was not detected

EST

No EST(s) were mapped for retro_hsap_3771 retrocopy.

TSS

No TSS is located nearby retro_hsap_3771 retrocopy 5' end.

Lab

retro_hsap_3771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3771 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2557
Gorilla gorilla	retro_ggor_2537
Pongo abelii	retro_pabe_3083
Macaca mulatta	retro_mmul_1637

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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	0.28 RPM
CEU_NA11843	0.54 RPM
CEU_NA11930	0.62 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	0.77 RPM
CEU_NA12751	1.75 RPM
CEU_NA12760	1.26 RPM
CEU_NA12827	0.33 RPM
CEU_NA12872	0.63 RPM
CEU_NA12873	0.80 RPM
FIN_HG00183	0.80 RPM
FIN_HG00277	0.81 RPM
FIN_HG00315	1.44 RPM
FIN_HG00321	1.21 RPM
FIN_HG00328	0.66 RPM
FIN_HG00338	0.34 RPM
FIN_HG00349	0.40 RPM
FIN_HG00375	2.15 RPM
FIN_HG00377	0.45 RPM
FIN_HG00378	0.89 RPM
GBR_HG00099	0.35 RPM
GBR_HG00111	0.64 RPM
GBR_HG00114	0.32 RPM
GBR_HG00119	1.20 RPM
GBR_HG00131	1.41 RPM
GBR_HG00133	0.87 RPM
GBR_HG00134	0.72 RPM
GBR_HG00137	0.88 RPM
GBR_HG00142	0.33 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.65 RPM
TSI_NA20513	0.36 RPM
TSI_NA20518	0.22 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.73 RPM
TSI_NA20765	1.02 RPM
TSI_NA20771	0.57 RPM
TSI_NA20786	0.84 RPM
TSI_NA20798	0.65 RPM
YRI_NA18870	0.37 RPM
YRI_NA18907	0.28 RPM
YRI_NA18916	0.57 RPM
YRI_NA19093	0.18 RPM
YRI_NA19099	0.48 RPM
YRI_NA19114	0.73 RPM
YRI_NA19118	0.25 RPM
YRI_NA19213	0.62 RPM
YRI_NA19214	0.39 RPM
YRI_NA19223	0.76 RPM

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Indel association:

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