RetrogeneDB ID: retro_pabe_3495

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:90149854..90150299(-)
• Located in intron of: ENSPPYG00000019399

Retrocopy information

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

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSPPYG00000001523
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_pabe_3495
TGTATGAGAGTAGTACCCCAGGAGCTCCTGCAAGACCTAGTGCCAGTACCAGTGTCCCTGGTGATGGAACGTTCAGAGGA
GCTCAACAACGACCTAAACCCCTTTACTCCTCTTATAAGGTATCCGGATTCCTGATTATGCCTTTATGCAAGACTTGGCC
AAGATGTATGAGCATCCTCTTGCTCTCACTAGTGCCAACCTCAGCTCCCAGGACAGTTCTCTGAATGTCATGGAGTTATA
AGACCTCTGGCCTCAGTTGTCCTTGGTCATTGAGGGGGGACAAACTAGGGATAGCCAGATCCCTGAGTGTTGCCTTGGCT
CAACTGTGGTTGACTTATCTGTGCATAGAAAGTTTGGCATCATTCGTCCAGGCTGTGCCCTGGAAAGTACTACAGCTTTC
CTTCAACAGAGGTATGGGTTGCACCCCTCACGTGCATCCTACTTG

Alignment

ORF - retro_pabe_3495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CRVRVPEGLLKDLLPGPVTLVMERSEELNKDLNPFTPLV-GIRIPDHAFMQDLAQMFEGPLALTSANLSS
          C...VP..LL.DL.P.PV.LVMERSEELN.DLNPFTPL..GIRIPD.AFMQDLA.M.E.PLALTSANLSS
Retrocopy CMRVVPQELLQDLVPVPVSLVMERSEELNNDLNPFTPLI>GIRIPDYAFMQDLAKMYEHPLALTSANLSS

Parental  QASSLNVEEFQDLWPQLSLVIDGGQIGDGQSPECRLGSTVVDLSVPGKFGIIRPGCALESTTAILQQKYG
          Q.SSLNV.E..DLWPQLSLVI.GGQ..D.Q.PEC.LGSTVVDLSV..KFGIIRPGCALESTTA.LQQ.YG
Retrocopy QDSSLNVMEL*DLWPQLSLVIEGGQTRDSQIPECCLGSTVVDLSVHRKFGIIRPGCALESTTAFLQQRYG

Parental  LLPSHVSYL
          L.PS..SYL
Retrocopy LHPSRASYL

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	5.75 RPM
SRP007412_cerebellum	0.00 RPM	6.44 RPM
SRP007412_heart	0.00 RPM	1.54 RPM
SRP007412_kidney	0.03 RPM	4.51 RPM
SRP007412_liver	0.00 RPM	4.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3495 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3495 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4289
Macaca mulatta	retro_mmul_1206

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495 ,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,