RetrogeneDB ID: retro_hsap_1869

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 18:10636666..10637398(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000265038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSG00000140650
• Aliases: PMM2, CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2
• Description: phosphomannomutase 2 [Source:HGNC Symbol;Acc:9115]

Sequence

>retro_hsap_1869
ATGGCAGCACCCGGCCCAGTGCTCTGCCTTTTGGACGTTGATGGGACCCTGACCACCCCGCAGCAGAAAATTACCAAAGA
AATGGATGACTTCCTACAAAAATTGAGGCAGAAGATCAAAATCGGAGTGGTAGGCAGGTTGGACTTTGAGGAAGCGCAGG
AGCAACTGGGAAATGCTGTGGTTGAAAAATATGATTACGTGTTTCCAGAAAATGGCTTGGTAGCACACAAACATGGGAAA
TCCTCGTGTAAATGGAATATTCAAAGTCACCTGGGTGAGGTCCAAATCCAAGATTTAATCAACTATTGTCTGAGCTGCAA
TGCAAAAATTAAACTCCTGAAGAAGAGGGGTACTTTAATTGAATTCTGAAATGGGATGTTAAACATGTCCCCTATTTGGA
AGAAGCTGCAGACAAGAAGAATGCATTGAGTTCTATGAATTCAATAAAAGAGAAAATATAAGAGAAAAAGTTGTAGCAGA
TCAAGGAAAGAGTTTGCAGGAAAAGCCCTCATGTTTTTCACAGGAGGCCAGATCAGCTTTGATGTCTTTCCTGATGGATG
GGGCAAGAGGTATTGCCTGTGACATGTGAAAAACGACGGTTATAAAGCCATTTATTTCTTTGGAGACAAAATCATACCAG
GTGGCAACGACCACGAGACCTTCACAGACTCCAGAACCGTGGGCTACTCCATGACTGTGCCTGAGGACACACGCAGGATC
TGTGAAGAGCTT

Alignment

ORF - retro_hsap_1869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPGPALCLFDVDGTLTAPRQKITKEMDDFLQKLRQKIKIGVVGGSDFEKVQEQLGNDVVEKYDYVFPE
          MAAPGP.LCL.DVDGTLT.P.QKITKEMDDFLQKLRQKIKIGVVG..DFE..QEQLGN.VVEKYDYVFPE
Retrocopy MAAPGPVLCLLDVDGTLTTPQQKITKEMDDFLQKLRQKIKIGVVGRLDFEEAQEQLGNAVVEKYDYVFPE

Parental  NGLVAYKDGKLLCRQNIQSHLGEALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI-GRSCSQE
          NGLVA.K.GK..C..NIQSHLGE..IQDLINYCLS..AKIKL.KKRGT.IEF.NGMLN.SPI.GRSC.QE
Retrocopy NGLVAHKHGKSSCKWNIQSHLGEVQIQDLINYCLSCNAKIKLLKKRGTLIEF*NGMLNMSPI>GRSCRQE

Parental  ERIEFYELDKKENIRQKFVAD-LRKEFAGKGLTFSIGGQISFDVFPDGWDKRYCLRHVENDGYKTIYFFG
          E.IEFYE..K.ENIR.K.VAD..RKEFAGK.L.F..GGQISFDVFPDGW.KRYCL.HV.NDGYK.IYFFG
Retrocopy ECIEFYEFNKRENIREKVVAD<SRKEFAGKALMFFTGGQISFDVFPDGWGKRYCL*HVKNDGYKAIYFFG

Parental  DKTMPGGNDHEIFTDPRTMGYSVTAPEDTRRICELL
          DK..PGGNDHE.FTD.RT.GYS.T.PEDTRRICE.L
Retrocopy DKIIPGGNDHETFTDSRTVGYSMTVPEDTRRICEEL

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	13.04 RPM
bodymap2_adrenal	0.00 RPM	15.17 RPM
bodymap2_brain	0.00 RPM	3.87 RPM
bodymap2_breast	0.00 RPM	7.57 RPM
bodymap2_colon	0.00 RPM	3.91 RPM
bodymap2_heart	0.00 RPM	3.71 RPM
bodymap2_kidney	0.00 RPM	8.05 RPM
bodymap2_liver	0.00 RPM	11.66 RPM
bodymap2_lung	0.00 RPM	5.15 RPM
bodymap2_lymph_node	0.00 RPM	5.30 RPM
bodymap2_ovary	0.00 RPM	9.33 RPM
bodymap2_prostate	0.00 RPM	6.51 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.89 RPM
bodymap2_testis	0.00 RPM	3.94 RPM
bodymap2_thyroid	0.00 RPM	12.32 RPM
bodymap2_white_blood_cells	0.00 RPM	7.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1869 was not detected

EST

No EST(s) were mapped for retro_hsap_1869 retrocopy.

TSS

No TSS is located nearby retro_hsap_1869 retrocopy 5' end.

Lab

retro_hsap_1869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1869 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1279

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000235	1 retrocopy	retro_cpor_810,
Homo sapiens	ENSG00000140650	2 retrocopies	retro_hsap_1869 , retro_hsap_1913,
Gorilla gorilla	ENSGGOG00000010124	1 retrocopy	retro_ggor_1399,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Nomascus leucogenys	ENSNLEG00000010062	1 retrocopy	retro_nleu_3062,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Pongo abelii	ENSPPYG00000007084	2 retrocopies	retro_pabe_1583, retro_pabe_1584,
Pan troglodytes	ENSPTRG00000007748	2 retrocopies	retro_ptro_1249, retro_ptro_1279,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,

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).