RetrogeneDB ID: retro_pabe_1938

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:34343323..34343929(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSPPYG00000005567
• Aliases: None
• Description: purine nucleoside phosphorylase [Source:HGNC Symbol;Acc:7892]

Sequence

>retro_pabe_1938
ATGGAGAATGGATACACATATGAAGATTATCAGAGCACTGCAGAATGGCTTCTGTTTCACACCAAGCACTGAACACAGGT
GACAGTGATCTGTGGGTCTGAATTAGGAGATCTGACTGACAAATTAATTCAGGCCCAAATCTTTAACAACAGTGAGATGC
TCAACTTTTTCCAAAGTACATTGCCAGGTCATGCTGGTTGACTGGTGTTTGGGTTCCTGAATGGCACAGCATGTGTGATG
ATGCAAGGAAGGTTCTACATGTATGATGGGTACCTGCTCTGGAACATGACATTTTCACATGAGGTTTTCCAGCTTCTGGG
TGGGAACATCTTGGTGGCCACCGATGCAGCTGGAGGGCTCAACCCCAAGTCTGGGGTTGGAAGGATCATGCTTCTCTGTG
ATCACATCAAGCTACTTGGTTTCTGTGATCAGAACTCTCCCAAAGCGCCCAATGATGAAAGGTTTGGAGTTCATTTTCCT
GCCACGTCTGATGCCTACTACTGGACAATGAGGCAAAAGGCGCTCAATTCTTAGAACCAAATGGGGAAGCAGCAAGAGGT
ACAGAAAGGCACCTGTGTGATGGCAGTAAACTGCAACTTTGAGACC

Alignment

ORF - retro_pabe_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.82 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYSEIPNFPRSTVPGHAGRLVF
          MENGYTYEDY..TAEWLL.HTKH..QV..ICGS.LG.LTDKL.QAQIF..SE..NF..ST.PGHAG.LVF
Retrocopy MENGYTYEDYQSTAEWLLFHTKH*TQVTVICGSELGDLTDKLIQAQIFNNSEMLNFFQSTLPGHAG*LVF

Parental  GFLNGRACVMMQGRFHMYEGYSLWKVTFPVRVFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLPG
          GFLNG.ACVMMQGRF.MY.GY.LW..TF...VF.LLG...LV.T.AAGGLNPK..VG.IML..DHI.L.G
Retrocopy GFLNGTACVMMQGRFYMYDGYLLWNMTFSHEVFQLLGGNILVATDAAGGLNPKSGVGRIMLLCDHIKLLG

Parental  FSGQNPLRGPNDERFGVRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMIAGPSFET
          F..QN....PNDERFGV.FPA.SDAY..TMRQ.AL....QMG.Q.E.Q.GT.VM.....FET
Retrocopy FCDQNSPKAPNDERFGVHFPATSDAYYWTMRQKALNS*NQMGKQQEVQKGTCVMAVNCNFET

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	13.60 RPM
SRP007412_cerebellum	0.00 RPM	15.44 RPM
SRP007412_heart	0.00 RPM	12.25 RPM
SRP007412_kidney	0.00 RPM	63.05 RPM
SRP007412_liver	0.00 RPM	47.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1938 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1938 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938 ,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,