RetrogeneDB ID: retro_pabe_204

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:62017676..62018732(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005879
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DKFZP459B0431
• Ensembl ID: ENSPPYG00000016782
• Aliases: TMEM30A, CDC50A
• Description: Cell cycle control protein 50A [Source:UniProtKB/Swiss-Prot;Acc:Q5R6C0]

Sequence

>retro_pabe_204
ATGACCTGGAGCGCCACGGCCCGGGGCGCCCACCAGCCCGACAACACCGCCTTCACGCAGCAGCGCCTCCCCGCCTGGCA
GCCGCTGCTGTCGGCCAGCATCGCGCTGCCGCTCTTCTTCTGCGCGGGCCTGGCCTTCATCGGCCTGGGCCTGGGCCTCT
ACTACTCCTCCAACGGCATCAAGGAGCTGGAGTACGACTACACAGGAGACCCGGGCACCGGCAACTGCTCGGTGTGCGCC
GCGGCCGGCCAGGGCCGGGCGCTGCCGCTCCCCTGCTCGTGCGCCTGGTACTTCTCGCTGCCCGAGCTCTTCCAGGGCCC
GGTGTACCTCTACTACGAGCTGACCAACTTCTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACGCGCAGCTGA
GCGGACTCCCCAGCGCGCTGCGCCACCCTGTCAACGAGTGCGCCCCCTACCAGCGCAGCGCGGCCGGCCTGCCCATCGCG
CCCTGCGGCGCCATCGCCAACAGCCTCTTCAACGACTCCTTCTCGCTTTGGCACCAGCGCCAGCCCGGCGGGCCCTATGT
CAAGGTGCCGCTCGACCGCTCCGGCATCGCCTGGTGGACCGACTACCACGTCAAGTTCCGCAACCCGCCGCTGGTCAATG
GCAGCCTGGCGTTGGCCTTCCAGGGCACGGCGCCCCCGCCCAACTGGCACCGGCCGGTCTACGAGCTGAGCCCCGACCCC
AACAACACCGGTTTCATCAATCAGGACTTCGTGGTGTGGATGCGCACGGCGGCTCTGCCCACGTTCCGCAAGCTGTACGC
GCGCATCCGCCAGGGCAACTACTCGGCCGGGCTGCCGCGGGGCGCCTACCGCGTCAACATCACCTACAACTACCCGGTGC
GCGCGTTCGGCGGCCACAAGCTCCTCATCTTCAGCAGCATCTCGTGGATGGGTGGCAAGAACCCCTTCCTGGGCATCGCC
TACCTGGTCGTCGGCTCCGTCTGCATCCTTACCGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGGACGA
CGACGACGAGGAGTGA

Alignment

ORF - retro_pabe_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.43 %
• Parental protein coverage: 55.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PCICTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNE-DKPIA
          PC.C...F.L...F.G.V..YY.L.NFYQN.RRY..SRDD.QL.G..SAL..P..EC.PY.R.....PIA
Retrocopy PCSCAWYFSLPELFQGPVYLYYELTNFYQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIA

Parental  PCGAIANSMFNDTLELFLIGNDSYP-IPIALKKKGIAWWTDKNVKFRNPP-GGDNLKERFKGTTKPVNWL
          PCGAIANS.FND...L........P.....L...GIAWWTD..VKFRNPP.....L...F.GT..P.NW.
Retrocopy PCGAIANSLFNDSFSLWHQRQPGGPYVKVPLDRSGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWH

Parental  KPVYMLDSDPDNNGFINEDFIVWMRTAALPTFRKLYRLIERKSDLHPTLPAGRYSLNVTYNYPVHYFDGR
          .PVY.L..DP.N.GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..N.TYNYPV..F.G.
Retrocopy RPVYELSPDPNNTGFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGAYRVNITYNYPVRAFGGH

Parental  KRMILSTISWMGGKNPFLGIAYIAVGSISFLLGVVLLVINHKYRNSSN
          K..I.S.ISWMGGKNPFLGIAY..VGS...L.G.V.LV....Y.....
Retrocopy KLLIFSSISWMGGKNPFLGIAYLVVGSVCILTGFVMLVVYIRYQDQDD

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	0.06 RPM	170.57 RPM
SRP007412_cerebellum	0.00 RPM	174.50 RPM
SRP007412_heart	0.03 RPM	42.78 RPM
SRP007412_kidney	6.20 RPM	86.68 RPM
SRP007412_liver	1.35 RPM	64.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_204 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204 ,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,