RetrogeneDB ID: retro_pabe_1933

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:20995638..20996065(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2D
• Ensembl ID: ENSPPYG00000012759
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide D [Source:HGNC Symbol;Acc:9191]

Sequence

>retro_pabe_1933
ATGGCAGCAGGCGGCAGCGATCTGCGGGCTGGCGATGTAGAGGAGGACGCTTCACAGCTCCTTTTTCCTAAAGAGTTTCA
AACAGCGGAGACCGTTCTAAATTCAGAAGTTCATATACTTCTGGAACAACGAAAGCAATAGAACAAGAGTGCAGAGGATG
AACAGGAACTCTCAGAAGTCTTCATGAAAACAATGAAACTACACAGGCTGTTTCAGTGGTTTCGAAAATAGAGAGACCAT
TGCCAGTGTTCGTAGCTTCTTACTCTAGAAAAACCTTCATAAATTTGAGTTGGTCTGTTTGGCCAACCTTTGCCCAGAGA
CTGCTGAGGAGTCCAAGGCTCTAATCCCAAACTTGGAGGGGTGGTTTGAAGATGAGGAGCTGCAGCAGATTCTTGATGAT
ATCCAGACAAAGCACAGCTTCCAGTAT

Alignment

ORF - retro_pabe_1933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTL-NYTA
          MAAGGSD.RAGDVEEDASQL.FPKEF.TAET.LNSEVH.LLE.RKQ.N.SAEDEQELSEVFMKT..NYT.
Retrocopy MAAGGSDLRAGDVEEDASQLLFPKEFQTAETVLNSEVHILLEQRKQ*NKSAEDEQELSEVFMKTM>NYTG

Parental  RFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRS
          .FS.F.NRETIASVRS.LL.K.LHKFEL.CLANLCPETAEESKALIP.LEG.FEDEELQQILDDIQTK.S
Retrocopy CFSGFENRETIASVRSFLL*KNLHKFELVCLANLCPETAEESKALIPNLEGWFEDEELQQILDDIQTKHS

Parental  FQY
          FQY
Retrocopy FQY

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	44.67 RPM
SRP007412_cerebellum	0.00 RPM	61.65 RPM
SRP007412_heart	0.00 RPM	22.85 RPM
SRP007412_kidney	0.00 RPM	28.11 RPM
SRP007412_liver	0.00 RPM	25.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1933 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1933 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1571
Gorilla gorilla	retro_ggor_1658
Macaca mulatta	retro_mmul_1011

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233, retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933 ,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,