RetrogeneDB ID: retro_ptro_1249

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:4363177..4363903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSPTRG00000007748
• Aliases: None
• Description: Phosphomannomutase 2 [Source:UniProtKB/TrEMBL;Acc:K7CN12]

Sequence

>retro_ptro_1249
ATGGCAGCACCCGGCCCAGTGCTCTGCCTTTTGGATGTTGATGGGACCCTGACCACCCTGCAGCAGAAAATTACCAAAGA
AATGGATGACTTCCTACAAAAATTGAGGCAGCAGATCAAAATCGGAGTGGTAGGCAGGTTGGACTTTGAGGAAGCGCAGG
AGCAACTGGGAAATGCTGTGGTTGAAAAATATGATTACGCGTTTCCAGAAAATGGCTTGGTAGCATACAAAGATGGGAAA
TCCTCGTGTAAATGGAATATTCAAAGTCACCTGGGTGAGGTCCAAATCCAAGATTTAATCAACTATTGTCTGAGCTGCAA
TGCAAAAATTAAACTCCTGAAGAAGAGGGGTACTTTCATTGAATTCTGAAATGGGATGTTAAACATGTCCCCTATTTGGA
AGAAGCTGCAGACAAGAAGAATGCATTGAGTTCTACGAATTCAATAAAAGAGAAAATATAAGAGAAAAAGCTGTAGCAGA
TCAAGGAAAGAGTTTGCAGGAAAAGCCCTCACGTTTTTCGTAGGAGGCCAGATCGGCTTTGATGTCTTTCCTGACAGATG
GGGCAAGAGGTATTGCCTGTGACATGTGAAAAATGACGGTTATAAGGCCATTTATTTCTTTGGAGACAAAATCATACCAG
GTGGCAACGACCACGAGACCTTCACAGACTCCAGAACCGTGGGCTACTCCATGACGGTGCCTGAGGACACACGCAGGATC
TGTGAA

Alignment

ORF - retro_ptro_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 98.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPGPALCLFDVDGTLTAPRQKITKEMDDFLQKLRQKIKIGVVGGSDFEKVQEQLGNDVVEKYDYVFPE
          MAAPGP.LCL.DVDGTLT...QKITKEMDDFLQKLRQ.IKIGVVG..DFE..QEQLGN.VVEKYDY.FPE
Retrocopy MAAPGPVLCLLDVDGTLTTLQQKITKEMDDFLQKLRQQIKIGVVGRLDFEEAQEQLGNAVVEKYDYAFPE

Parental  NGLVAYKDGKLLCKQNIQSHLGEALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI-GRSCSQE
          NGLVAYKDGK..CK.NIQSHLGE..IQDLINYCLS..AKIKL.KKRGTFIEF.NGMLN.SPI.GRSC.QE
Retrocopy NGLVAYKDGKSSCKWNIQSHLGEVQIQDLINYCLSCNAKIKLLKKRGTFIEF*NGMLNMSPI>GRSCRQE

Parental  ERIEFYELDKKENIRQKFVAD-LRKEFAGKGLTFSIGGQISFDVFPDGWDKRYCLRHVENDGYKTIYFFG
          E.IEFYE..K.ENIR.K.VAD..RKEFAGK.LTF..GGQI.FDVFPD.W.KRYCL.HV.NDGYK.IYFFG
Retrocopy ECIEFYEFNKRENIREKAVAD<SRKEFAGKALTFFVGGQIGFDVFPDRWGKRYCL*HVKNDGYKAIYFFG

Parental  DKTMPGGNDHEIFTDPRTMGYSVTAP-DTRRICE
          DK..PGGNDHE.FTD.RT.GYS.T.P.DTRRICE
Retrocopy DKIIPGGNDHETFTDSRTVGYSMTVPEDTRRICE

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	1.86 RPM
SRP007412_cerebellum	0.00 RPM	4.41 RPM
SRP007412_heart	0.00 RPM	3.03 RPM
SRP007412_kidney	0.03 RPM	13.05 RPM
SRP007412_liver	0.00 RPM	14.66 RPM
SRP007412_testis	0.11 RPM	5.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1249 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1249 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1913
Gorilla gorilla	retro_ggor_1399
Pongo abelii	retro_pabe_1584

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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,