RetrogeneDB ID: retro_hsap_4332

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: GL000228.1:43060..43325(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RARRES2
• Ensembl ID: ENSG00000106538
• Aliases: RARRES2, HP10433, TIG2
• Description: retinoic acid receptor responder (tazarotene induced) 2 [Source:HGNC Symbol;Acc:9868]

Sequence

>retro_hsap_4332
AGACAGGGAAGCGGCTGGAGGAAGGCCTGGAAGAAACCCAAGTGCAAAGCCCAGCCCGAGAGGAGGAAGCAGAAATGCCT
GACCTGCGTCAAAATGGACTGTGAGGATAAGGTTCTGGGCAGGATGGTTCGCTGCCCTCCAGAGACGCAGACTCGGCGGG
AGCCTGAGGAGCACCAGGGGGCCGGGTGCAGCCCGGCGGAGCGGGCGGTGAGGACCCCACGGCTGCCGCTTCCCTGCACG
GTTCGCCTCCTCCAAGGCCCGGCCC

Alignment

ORF - retro_hsap_4332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQTSCRKRDWKKPECKVRPNGRKRKCLACIKLGSEDKVLGRLVHCPIETQVLREAEEHQETQCLRVQRA-
          .Q.S.....WKKP.CK..P..RK.KCL.C.K...EDKVLGR.V.CP.ETQ..RE.EEHQ...C....RA.
Retrocopy RQGSGWRKAWKKPKCKAQPERRKQKCLTCVKMDCEDKVLGRMVRCPPETQTRREPEEHQGAGCSPAERA<

Parental  GED-PHSFYFPGQFAFSKALP
          GED.PH...FP..FA.SKA.P
Retrocopy GED<PHGCRFPARFASSKARP

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	38.90 RPM
bodymap2_adrenal	0.00 RPM	78.66 RPM
bodymap2_brain	0.00 RPM	7.83 RPM
bodymap2_breast	0.00 RPM	230.96 RPM
bodymap2_colon	0.00 RPM	81.81 RPM
bodymap2_heart	0.00 RPM	2.88 RPM
bodymap2_kidney	0.00 RPM	44.61 RPM
bodymap2_liver	0.00 RPM	190.66 RPM
bodymap2_lung	0.00 RPM	209.11 RPM
bodymap2_lymph_node	0.00 RPM	72.40 RPM
bodymap2_ovary	0.00 RPM	81.50 RPM
bodymap2_prostate	0.00 RPM	97.53 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.93 RPM
bodymap2_testis	0.00 RPM	34.11 RPM
bodymap2_thyroid	0.00 RPM	29.24 RPM
bodymap2_white_blood_cells	0.00 RPM	0.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4332 was not detected

EST

No EST(s) were mapped for retro_hsap_4332 retrocopy.

TSS

No TSS is located nearby retro_hsap_4332 retrocopy 5' end.

Lab

retro_hsap_4332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4332 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010322	5 retrocopies	retro_cjac_2100, retro_cjac_2706, retro_cjac_3874, retro_cjac_3904, retro_cjac_4141,
Homo sapiens	ENSG00000106538	13 retrocopies	retro_hsap_1678, retro_hsap_1679, retro_hsap_1680, retro_hsap_1681, retro_hsap_1682, retro_hsap_1683, retro_hsap_2665, retro_hsap_3134, retro_hsap_4327, retro_hsap_4330, retro_hsap_4332 , retro_hsap_4792, retro_hsap_743,
Gorilla gorilla	ENSGGOG00000011158	1 retrocopy	retro_ggor_2984,
Macaca mulatta	ENSMMUG00000005232	4 retrocopies	retro_mmul_1555, retro_mmul_1993, retro_mmul_2378, retro_mmul_2554,
Nomascus leucogenys	ENSNLEG00000001362	18 retrocopies	retro_nleu_1108, retro_nleu_1744, retro_nleu_2079, retro_nleu_2944, retro_nleu_2978, retro_nleu_2999, retro_nleu_3000, retro_nleu_3001, retro_nleu_3034, retro_nleu_3036, retro_nleu_3067, retro_nleu_3071, retro_nleu_3072, retro_nleu_3076, retro_nleu_3089, retro_nleu_3092, retro_nleu_3119, retro_nleu_3128,
Pongo abelii	ENSPPYG00000018166	28 retrocopies	retro_pabe_1382, retro_pabe_1383, retro_pabe_1384, retro_pabe_1386, retro_pabe_1387, retro_pabe_1423, retro_pabe_1424, retro_pabe_1425, retro_pabe_1426, retro_pabe_2404, retro_pabe_2591, retro_pabe_2593, retro_pabe_2595, retro_pabe_2596, retro_pabe_2597, retro_pabe_2600, retro_pabe_2604, retro_pabe_2605, retro_pabe_2606, retro_pabe_2608, retro_pabe_3540, retro_pabe_3558, retro_pabe_3559, retro_pabe_3604, retro_pabe_3727, retro_pabe_638, retro_pabe_639, retro_pabe_666,
Pan troglodytes	ENSPTRG00000019854	10 retrocopies	retro_ptro_1095, retro_ptro_1096, retro_ptro_1097, retro_ptro_1098, retro_ptro_1099, retro_ptro_1100, retro_ptro_1795, retro_ptro_2942, retro_ptro_3067, retro_ptro_3188,

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).