RetrogeneDB ID: retro_hsap_3746

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:66254801..66255327(+)
• Located in intron of: ENSG00000243335

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSG00000109519
• Aliases: None
• Description: GrpE-like 1, mitochondrial (E. coli) [Source:HGNC Symbol;Acc:19696]

Sequence

>retro_hsap_3746
GTGGTGGCTCCATGCGTGAGGCTGGTGCCATGCAGTCTCCTGGTGTTGGCATTGTCTCCCAGCCTTCTCAGTTCTGCACA
CAGCTACAAAACAAAAGAACAGTTGCCAGCACTTGGAAGAGGATGTGGATCCAAACCAAATGGAGGACAGATACTCCCTC
TACGGACAAGATACTCATGGAAGAAGTCAAGTTAGAAGAGCAGCTGAAGGAGGCTGTAGAAGAAGATAAGCAAGCATTGG
CAGATACTGAGGACTTGCAGCAGATCAGCCAAAAATTGGTGGAGGAGGCAAATATGTATAGCATTCAGGGCTTCTGCAAG
GACTCGTTAGAGGTTGCAGATGTTTTGGAGAAGGCAACACAGTGTGTTCCAGAAGAAGAAATTAAAGACAATAACCCTCA
CCTGAAGAACCTCTGTGAAACTCTCAACAATGAGTGGAGTCCAGATTCAGGAAGTGTTCAGCAAGCACTGCCAAGCTGAA
CCCTGTCAGAGCCAAGTTCCACCCTTATGCGCATGAGGTCTTTTTT

Alignment

ORF - retro_hsap_3746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.75 %
• Parental protein coverage: 82.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAQCVRLARRSLPALALSLRPSP-RLLCTATKQKNSGQNLEEDMG-QSEQKADPPATEKTLLEEKVKLE
          ..A.CVRL...SL..L.L.L.PS....L.TATKQKNS.Q.LEED...Q.....D.P.T.K.L.EE.VKLE
Retrocopy VVAPCVRLVPCSL--LVLALSPSL>SVLHTATKQKNSCQHLEEDVD>QTKWRTDTPSTDKILMEE-VKLE

Parental  EQLKETVEKYKRALADTENLRQRSQKLVEEAKLYGIQAFCKDLLEVADVLEKATQCVPKEEIKDDNPHLK
          EQLKE.VE..K.ALADTE.L.Q.SQKLVEEA..Y.IQ.FCKD.LEVADVLEKATQCVP.EEIKD.NPHLK
Retrocopy EQLKEAVEEDKQALADTEDLQQISQKLVEEANMYSIQGFCKDSLEVADVLEKATQCVPEEEIKDNNPHLK

Parental  NLYEGL-VMTEVQIQKVFTKHGLLKLNPVGAKFDP-YEHEALF
          NL.E.L..M..VQIQ.VF.KH......P......P.Y.HE..F
Retrocopy NLCETL>TMSGVQIQEVFSKH--CQAEPCQSQVPP>YAHEVFF

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	0.14 RPM	36.69 RPM
bodymap2_adrenal	0.35 RPM	38.77 RPM
bodymap2_brain	0.07 RPM	36.38 RPM
bodymap2_breast	0.25 RPM	24.96 RPM
bodymap2_colon	0.15 RPM	41.28 RPM
bodymap2_heart	0.00 RPM	34.34 RPM
bodymap2_kidney	0.15 RPM	56.40 RPM
bodymap2_liver	0.00 RPM	65.84 RPM
bodymap2_lung	0.09 RPM	30.52 RPM
bodymap2_lymph_node	0.07 RPM	31.43 RPM
bodymap2_ovary	0.19 RPM	40.15 RPM
bodymap2_prostate	0.21 RPM	31.12 RPM
bodymap2_skeletal_muscle	0.00 RPM	37.70 RPM
bodymap2_testis	0.40 RPM	44.66 RPM
bodymap2_thyroid	0.13 RPM	31.98 RPM
bodymap2_white_blood_cells	0.00 RPM	31.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3746 was not detected

EST

No EST(s) were mapped for retro_hsap_3746 retrocopy.

TSS

No TSS is located nearby retro_hsap_3746 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CCATGCAGTCTCCTGGTGTTG (21 nt long)
• Reverse primer: GCCCATGCTTGAACCTCACT (20 nt long)
• Anneling temperature: 60 °C
• (Expected) product size: 712
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3746 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2544

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746 , retro_hsap_3864, retro_hsap_3870,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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