RetrogeneDB ID: retro_pabe_2198

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:12178155..12178428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP1
• Ensembl ID: ENSPPYG00000005083
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 1 [Source:HGNC Symbol;Acc:14002]

Sequence

>retro_pabe_2198
TCACCTTCTACCCATGTGGTATTATTCTCACAGTACCACCAGCTGCTGAGTGACTATGGGCCACCATCCCTAGGCTATAC
CCAGGGAACTGGAAACAGCTAAGTGACCCCAAAGCAAATGTGCTAAACTGCTGGCTATCATCCAAGAGCTGAGGGAGCTA
TCAGATCCACCTATACAGGAAGCAAGAGCACAATGAAGAGACCAAAACAAGTTATCATTCATGCTAAAAGACTAGTTTGG
GAGAGCTTGGCTAAAACAGAATGGAATGCCAGA

Alignment

ORF - retro_pabe_2198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.82 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPSSSMATSSQYRQLLSDYGPPSLGYTQGTGNSQV-PQSKYAELLAIIEELGK-EIRPTYAGSKSAMERL
          SPS......SQY.QLLSDYGPPSLGYTQGTGNS.V.PQSK.A.LLAII.EL....IR.TY.GSKS.M.R.
Retrocopy SPSTHVVLFSQYHQLLSDYGPPSLGYTQGTGNS*V>PQSKCAKLLAIIQELRE<AIRSTYTGSKSTMKRP

Parental  KRGIIHARGLVRECLAETERNAR
          K..IIHA..LV.E.LA.TE.NAR
Retrocopy KQVIIHAKRLVWESLAKTEWNAR

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	31.90 RPM
SRP007412_cerebellum	0.00 RPM	34.29 RPM
SRP007412_heart	0.00 RPM	10.69 RPM
SRP007412_kidney	0.00 RPM	15.71 RPM
SRP007412_liver	0.00 RPM	10.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2198 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2198 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2834
Pan troglodytes	retro_ptro_1921
Gorilla gorilla	retro_ggor_1968
Macaca mulatta	retro_mmul_1507

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015147	1 retrocopy	retro_amel_19,
Choloepus hoffmanni	ENSCHOG00000010939	1 retrocopy	retro_chof_56,
Dasypus novemcinctus	ENSDNOG00000017145	21 retrocopies	retro_dnov_1094, retro_dnov_1097, retro_dnov_1236, retro_dnov_1502, retro_dnov_1569, retro_dnov_1656, retro_dnov_1750, retro_dnov_1979, retro_dnov_2000, retro_dnov_2145, retro_dnov_2249, retro_dnov_2527, retro_dnov_2661, retro_dnov_2662, retro_dnov_2673, retro_dnov_270, retro_dnov_687, retro_dnov_69, retro_dnov_70, retro_dnov_729, retro_dnov_741,
Felis catus	ENSFCAG00000026822	1 retrocopy	retro_fcat_1578,
Homo sapiens	ENSG00000111328	2 retrocopies	retro_hsap_2227, retro_hsap_2834,
Gorilla gorilla	ENSGGOG00000009567	1 retrocopy	retro_ggor_1968,
Macropus eugenii	ENSMEUG00000009438	12 retrocopies	retro_meug_1101, retro_meug_1112, retro_meug_1218, retro_meug_1366, retro_meug_1509, retro_meug_1565, retro_meug_2116, retro_meug_377, retro_meug_404, retro_meug_669, retro_meug_836, retro_meug_868,
Monodelphis domestica	ENSMODG00000012451	2 retrocopies	retro_mdom_1845, retro_mdom_611,
Mustela putorius furo	ENSMPUG00000001667	1 retrocopy	retro_mputfur_1601,
Mus musculus	ENSMUSG00000029394	1 retrocopy	retro_mmus_125,
Nomascus leucogenys	ENSNLEG00000001478	2 retrocopies	retro_nleu_1209, retro_nleu_2686,
Otolemur garnettii	ENSOGAG00000024823	1 retrocopy	retro_ogar_2292,
Pongo abelii	ENSPPYG00000005083	2 retrocopies	retro_pabe_1974, retro_pabe_2198 ,
Pan troglodytes	ENSPTRG00000005596	3 retrocopies	retro_ptro_1574, retro_ptro_1921, retro_ptro_2929,
Pteropus vampyrus	ENSPVAG00000015302	1 retrocopy	retro_pvam_478,
Rattus norvegicus	ENSRNOG00000001070	3 retrocopies	retro_rnor_1717, retro_rnor_1718, retro_rnor_1753,
Sarcophilus harrisii	ENSSHAG00000015009	1 retrocopy	retro_shar_366,
Sus scrofa	ENSSSCG00000009775	2 retrocopies	retro_sscr_992, retro_sscr_993,
Tursiops truncatus	ENSTTRG00000015881	2 retrocopies	retro_ttru_312, retro_ttru_464,