RetrogeneDB ID: retro_pabe_1583

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:21495936..21496667(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSPPYG00000007084
• Aliases: None
• Description: phosphomannomutase 2 [Source:HGNC Symbol;Acc:9115]

Sequence

>retro_pabe_1583
ATGGCAGCACCCGGCCCAGTGCTCTGCCTTTTGGATGTTGATGGGACCCTGACCACCCCACAGCAGAAAATTACCAAAGA
AATGGATGACTTCCTACAAAAATTGAGGCAGAAGATCAAAATCGGAGTGGTGGGCACGTTGGACTTTGAGGAAGCACAGG
AGCAACTGGGAAATGATGTGGTTGAAAAATATGATTATGCGTTTCCAGAAAATGGCTTGGTAGCATACAAAGATGGGAAA
TGCTCGTGTAAATGGAATATTCAAAGTCACCTGGGTGAGGTCCTAATCCAAGATTTAATCAACTATTGTCTGAGCTGCAA
TGCAAAAATTAAACTCCTGAAGAAAAGGGGTACTTTCATTGAATTCTGAAATGGGATGTTAAACATGTCCCCTATTTGGA
AGAAGCTGCAGCCAAGAAGAATGCATTGAGTTCTACGAATTCAATAAAAAAGAAAATATAAGAGAAAAAGTTGTAGCAGA
TCAAGGAAAGAGTTTGCAGGAAAAGGCCTCACGTTTTCCTAGAAGGCCAGATCAGCTTTGATGTCTTTCCTGATGGATGG
GGCAAGAGGTATTGCCTGTGACATGTGAAAAACGACGGTTATAAGGCCATTTATTTCTTTGGAGACAAAATCATACCAGG
TGGCAACAACCATGAGACCTTCACAGACTCCAGAACCGTGGGCTACTCCATGACGGTGCCTGAGGACACACGCAGGATCT
GTGAAGAGCTT

Alignment

ORF - retro_pabe_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPGPALCLFDVDGTLTAPRQKITKEMDDFLQKLRQKIKIGVVGGSDFEKVQEQLGNDVVEKYDYVFPE
          MAAPGP.LCL.DVDGTLT.P.QKITKEMDDFLQKLRQKIKIGVVG..DFE..QEQLGNDVVEKYDY.FPE
Retrocopy MAAPGPVLCLLDVDGTLTTPQQKITKEMDDFLQKLRQKIKIGVVGTLDFEEAQEQLGNDVVEKYDYAFPE

Parental  NGLVAYKDGKLLCKQNIQSHLGEALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI-GRSCSQE
          NGLVAYKDGK..CK.NIQSHLGE.LIQDLINYCLS..AKIKL.KKRGTFIEF.NGMLN.SPI.GRSCSQE
Retrocopy NGLVAYKDGKCSCKWNIQSHLGEVLIQDLINYCLSCNAKIKLLKKRGTFIEF*NGMLNMSPI>GRSCSQE

Parental  ERIEFYELDKKENIRQKFVAD-LRKEFAGKGLTFS-IGGQISFDVFPDGWDKRY-LRHVENDGYKTIYFF
          E.IEFYE..KKENIR.K.VAD..RKEFAGKGLTFS...GQISFDVFPDGW.KRY.L.HV.NDGYK.IYFF
Retrocopy ECIEFYEFNKKENIREKVVAD<SRKEFAGKGLTFS<LEGQISFDVFPDGWGKRYCL*HVKNDGYKAIYFF

Parental  GDKTMPGGNDHEIFTDPRTMGYSVTAPEDTRRICEVL
          GDK..PGGN.HE.FTD.RT.GYS.T.PEDTRRICE.L
Retrocopy GDKIIPGGNNHETFTDSRTVGYSMTVPEDTRRICEEL

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	0.22 RPM	2.65 RPM
SRP007412_cerebellum	0.61 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	0.63 RPM
SRP007412_kidney	0.00 RPM	5.87 RPM
SRP007412_liver	0.00 RPM	2.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1583 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1583 has 0 orthologous retrocopies within eutheria group .

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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,