RetrogeneDB ID: retro_hsap_3363

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:109220643..109221075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000253224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSG00000247077
• Aliases: PGAM5, BXLBV68
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_hsap_3363
GCTGGCACAGTGGGGAAGCCGCGCGCAGCCGAGGCGCCGGCCTGGGCGTGGGGCACGCGGCCGAGCCTCAGCGTCTGGGA
CCCCGACCGGGACAGGCAAGAACCACTGTCTCTGAACAACCTAAGGAAGAGGAACGTGGAATCTGGAGAATAGCTGGCTT
CCAGGCTGGACCACTGCAGAGCCAAGGCCACAGGGCACACCCTCCTCGTCATGCGTTCCCAATACCATGTGGACGGCTCC
CTGGAAAAGGACTGCAGTCTGAACCCACTGGGTCGTGAACAGGTCGAACTAACTGGACTCCGACTTGCAAGCTTGGGGTT
GAGGTTTAATAAAATCGTCCATTCCTCCATGACCCACCCCATAGAAACCACTGGCTTCAGCAACAGGCACCTGCCAAGCG
TCTTCAAAGGCCGCACAGACCTGGGGCGGGAA

Alignment

ORF - retro_hsap_3363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 56.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGGDAEPRPAEPPAWAGGARPGPGVWDPNWDRREPLSLINVRKRNVESGEEELASKLDHYKAKATRHIFL
          AG....PR.AE.PAWA.G.RP...VWDP..DR.EPLSL.N.RKRNVESGE..LAS.LDH..AKAT.H..L
Retrocopy AGTVGKPRAAEAPAWAWGTRPSLSVWDPDRDRQEPLSLNNLRKRNVESGE*-LASRLDHCRAKATGHTLL

Parental  IRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVST
          ...SQYHVDGSLEKD..L.PLGREQ.ELTGLRLASLGL.FNKIVHSSMT..IETT....RHLP.V.K..T
Retrocopy VMRSQYHVDGSLEKDCSLNPLGREQVELTGLRLASLGLRFNKIVHSSMTHPIETTGFSNRHLPSVFKGRT

Parental  DLLRE
          DL.RE
Retrocopy DLGRE

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	20.53 RPM
bodymap2_adrenal	0.00 RPM	23.83 RPM
bodymap2_brain	0.00 RPM	17.63 RPM
bodymap2_breast	0.00 RPM	16.19 RPM
bodymap2_colon	0.00 RPM	17.44 RPM
bodymap2_heart	0.00 RPM	16.71 RPM
bodymap2_kidney	0.00 RPM	25.95 RPM
bodymap2_liver	0.00 RPM	32.43 RPM
bodymap2_lung	0.00 RPM	15.07 RPM
bodymap2_lymph_node	0.00 RPM	23.66 RPM
bodymap2_ovary	0.00 RPM	25.64 RPM
bodymap2_prostate	0.00 RPM	19.71 RPM
bodymap2_skeletal_muscle	0.00 RPM	44.20 RPM
bodymap2_testis	0.06 RPM	27.53 RPM
bodymap2_thyroid	0.00 RPM	23.54 RPM
bodymap2_white_blood_cells	0.00 RPM	21.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3363 was not detected

EST

No EST(s) were mapped for retro_hsap_3363 retrocopy.

TSS

No TSS is located nearby retro_hsap_3363 retrocopy 5' end.

Lab

retro_hsap_3363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3363 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2286
Macaca mulatta	retro_mmul_2101

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363 ,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,

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

---

Indel association:

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