RetrogeneDB ID: retro_hsap_3319

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:54825986..54826529(-)
• Located in intron of: ENSG00000067113

Retrocopy information

• Ensembl ID: ENSG00000250853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSG00000134758
• Aliases: RNF138, HSD-4, NARF, STRIN, hNARF
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_hsap_3319
GAGAGAGCATGCCCTGAACGGGCCTTAGACCTTGAAAATATAATGAGGAAGTTTTCTGGTAGCTGCAGATGCTGTGCAAA
ACAGATTAAATTCTATCGCATGAGACTTCATTGCAAATCTTGTAAGAAGTATCAGGATGAATATGATGTTTCTTCTATCA
TTCCAAACTTTCAGATCTCTGAAGATTCAGTAGGGAACAGCAATAGGAGTGAAACATCCACATCTGATAACACAGAAACT
TACCAAGAGAATACAAGTTCTTCTGGTCATCCTACTTATAAGTGTCCCCTGTGTCAAGAATCAAATTTTACCAGAGAGCG
TTTACTGGATCACTCTAACAGTAATCACTTATTTCAGATAGTTCCTGTGACATGTCCTATTTGTGTATCTCTTCCTTGGG
GAGATCCTAGCCAGATTACCAGAAATTTCGTTAGTCATCTAAATCAGAGACATCAGTTTGATTATGGAGAATTTGTGAAT
CTTCAGCTAGATGAAGAAACTCAATGTCAAACTGCTGTTGAAGAATCATTTCAAGTAAACATC

Alignment

ORF - retro_hsap_3319 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.58 %
• Parental protein coverage: 73.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERACPERALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGNSNRS
          ERACPERALDLENIMRKFSGSCRCCAKQIKFYRMR.H.KSCKKYQDEY.VSSIIPNFQIS.DSVGNSNRS
Retrocopy ERACPERALDLENIMRKFSGSCRCCAKQIKFYRMRLHCKSCKKYQDEYDVSSIIPNFQISEDSVGNSNRS

Parental  ETSTSDNTETYQENTSSSGHPTFKCPLCQESNFTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPSQIT
          ETSTSDNTETYQENTSSSGHPT.KCPLCQESNFTR.RLLDH.NSNHLFQIVPVTCPICVSLPWGDPSQIT
Retrocopy ETSTSDNTETYQENTSSSGHPTYKCPLCQESNFTRERLLDHSNSNHLFQIVPVTCPICVSLPWGDPSQIT

Parental  RNFVSHLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          RNFVSHLNQRHQFDYGEFVNLQLDEETQ.QTAVEESFQVNI
Retrocopy RNFVSHLNQRHQFDYGEFVNLQLDEETQCQTAVEESFQVNI

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	0.72 RPM	27.15 RPM
bodymap2_adrenal	0.76 RPM	49.72 RPM
bodymap2_brain	0.07 RPM	28.97 RPM
bodymap2_breast	0.33 RPM	28.19 RPM
bodymap2_colon	0.06 RPM	24.31 RPM
bodymap2_heart	0.24 RPM	8.64 RPM
bodymap2_kidney	0.04 RPM	27.05 RPM
bodymap2_liver	0.08 RPM	13.14 RPM
bodymap2_lung	0.00 RPM	37.73 RPM
bodymap2_lymph_node	0.00 RPM	29.91 RPM
bodymap2_ovary	0.02 RPM	44.22 RPM
bodymap2_prostate	0.29 RPM	23.64 RPM
bodymap2_skeletal_muscle	0.15 RPM	12.44 RPM
bodymap2_testis	0.11 RPM	153.29 RPM
bodymap2_thyroid	0.30 RPM	30.05 RPM
bodymap2_white_blood_cells	0.00 RPM	89.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3319 was not detected

EST

1 EST(s) were mapped to retro_hsap_3319 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EC573729	54826219	54826323	99.1	100	1	96

TSS

No TSS is located nearby retro_hsap_3319 retrocopy 5' end.

Lab

retro_hsap_3319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3319 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2155
Pongo abelii	retro_pabe_2734

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319 ,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,

Population studies

Expression level across human populations :

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

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Indel association:

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