RetrogeneDB ID: retro_hsap_3898

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:124800262..124800599(-)
• Located in intron of: ENSG00000224897

Retrocopy information

• Ensembl ID: ENSG00000205898
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C11orf58
• Ensembl ID: ENSG00000110696
• Aliases: None
• Description: chromosome 11 open reading frame 58 [Source:HGNC Symbol;Acc:16990]

Sequence

>retro_hsap_3898
GAGTCCTATCCTCACAGGGTGAAGTGTTCAGTCTTCACAGACAACAATCTTGGACCTAGCAATTTGTAATTAGCAAACTT
AGGTAATGAAGAAAGAAAGTAAACATTCTTTAGACATGGGTGTAGAAAAGAAAGAACAAACTGGCCGTCTTGTTACAGGA
GATCAAAAATCAATATCTTACTTCTGAAAAGGGGAAGAAGACAAGAAAATTGATGAGGAACTGGAGTTTCAATATCAGCC
AGGTGTCAATAGTCAATTTTCAGGAAGGGACAGATGACACTGTGAACTTGGCTTTAGTGAAGTACATCATGATGAAGAAG
GTGATGTAGCTGGAGAG

Alignment

ORF - retro_hsap_3898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.74 %
• Parental protein coverage: 62.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLRLMGAGKK-EHTGRLVIGDHKSTSHFRTGEEDK
          ES.PH.VK.S...D..LG.SN...A.LGNEERK..F.R..G..K..E.TGRLV.GD.KS.S.F..GEEDK
Retrocopy ESYPHRVKCSVFTDNNLGPSNL*LANLGNEERK*TFFR-HGCRKE>EQTGRLVTGDQKSISYF*KGEEDK

Parental  KINEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGD
          KI.EELE.QYQ....S..SGR.R.HC.LGFSEV..HD.EGDVAG.
Retrocopy KIDEELEFQYQPGVNSQFSGRDR*HCELGFSEVH-HDEEGDVAGE

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	146.98 RPM
bodymap2_adrenal	0.00 RPM	148.51 RPM
bodymap2_brain	0.12 RPM	199.78 RPM
bodymap2_breast	0.00 RPM	145.25 RPM
bodymap2_colon	0.00 RPM	201.21 RPM
bodymap2_heart	0.07 RPM	119.04 RPM
bodymap2_kidney	0.19 RPM	135.09 RPM
bodymap2_liver	0.00 RPM	72.73 RPM
bodymap2_lung	0.00 RPM	151.86 RPM
bodymap2_lymph_node	0.00 RPM	143.76 RPM
bodymap2_ovary	0.15 RPM	216.75 RPM
bodymap2_prostate	0.23 RPM	195.44 RPM
bodymap2_skeletal_muscle	0.00 RPM	94.41 RPM
bodymap2_testis	0.00 RPM	169.83 RPM
bodymap2_thyroid	0.04 RPM	237.71 RPM
bodymap2_white_blood_cells	0.00 RPM	139.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3898 was not detected

EST

No EST(s) were mapped for retro_hsap_3898 retrocopy.

TSS

No TSS is located nearby retro_hsap_3898 retrocopy 5' end.

Lab

retro_hsap_3898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3898 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_3098

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898 ,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 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	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 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	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 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).