RetrogeneDB ID: retro_pabe_1369

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:77103540..77103899(+)
• Located in intron of: ENSPPYG00000007663

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSPPYG00000001380
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_pabe_1369
GAAATGGATCAGACAATGGCTGCCAATGCTAAGAATAAATTCTTAATTGATAAATTTCTAAGAAATCAAGACAACCTCCA
AGATTGGGCCAAGAGCATGGATGGGAAAGGCAGATGTGCATCTGGTTCTGTTTTCTGACCATAATAACGAGATCTGCATC
AAAGGATGTCTTGAGAGGAGGGAACAGTGGTAACAGTGAAGCCAGCAGAGAGAGCTTGGGAAAGAGAATTCAGACCCATC
TTCAAGTTAACAAAAACAATTACTGACTCATACGAAGAAATCGGGAAAGTCAATAAAGCAGATGCTTCTAAACCTGTTGA
TGAAGTTTTTCTGAAGTTGTGAAAATTTCCAACAAAAAA

Alignment

ORF - retro_pabe_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTMD-GKADVSFVLFFDCNNEICIERCLER-GKSSGRSD
          EMDQTMAANA.KNKFLID.F.RNQDNLQ.W.K.MD.GKADV..VLF.D.NNEICI..CLER.G.S.G.S.
Retrocopy EMDQTMAANA-KNKFLIDKFLRNQDNLQDWAKSMD>GKADVHLVLFSDHNNEICIKGCLER>GNS-GNSE

Parental  DNRESLEKRIQTYLQ-STKPIIDLYEEMGKVKKIDASKSVDEV-FDEVVQIFDKE
          ..RESL.KRIQT.LQ..TK.I.D.YEE.GKV.K.DASK.VDEV.F.EVV.I..K.
Retrocopy ASRESLGKRIQTHLQ>LTKTITDSYEEIGKVNKADASKPVDEV<FSEVVKISNKK

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	0.00 RPM	17.36 RPM
SRP007412_cerebellum	0.00 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	12.64 RPM
SRP007412_kidney	0.00 RPM	23.77 RPM
SRP007412_liver	0.03 RPM	32.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1369 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1369 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369 ,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373,