RetrogeneDB ID: retro_pabe_3043

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:8800967..8801360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAS2
• Ensembl ID: ENSPPYG00000025912
• Aliases: None
• Description: related RAS viral (r-ras) oncogene homolog 2 [Source:HGNC Symbol;Acc:17271]

Sequence

>retro_pabe_3043
TCCTATTTTTTAATGGATTCTGTTCCAACCGTTGCAGATTCCAACACAAAGCAGTGTGTGCTAGATGGAAGAGCAGCCCA
GCTATGTGTTTTGTAGACAACAGGACAAGAAGAGTTTGGAGTCATGAAGGAACAGTGTATGAGGACTGGTGAGAGTTTCC
TATCGGTCTTTTCAGGCACCAATAGAGGCAGTTTCGAAGAAACCTATAAATTCCAAAGACAGATTCTCCTCAGAGTAAAG
GACCATGGTGAGTTTCCAATGATTTTTATGGGTAATAAAGCAGCTCTGGATAATCAAAGACAGGAAACACAGGAAAAACA
GCATTTAGCACAGCAATGTAAGGTAATATACATGGAGGTATCAGCAAAGATTAGGATGAATGCAGAGGGTGCC

Alignment

ORF - retro_pabe_3043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 77.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYK
          SYF..D..PT..DS.TKQCV.D.RAA.L..L.T.GQEEFG.M.EQ.MRTGE.FL.VFS.T.RGSFEE.YK
Retrocopy SYFLMDSVPTVADSNTKQCVLDGRAAQLCVL*TTGQEEFGVMKEQCMRTGESFLSVFSGTNRGSFEETYK

Parental  FQRQIL-RVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQA
          FQRQIL.RVKD..EFPMI..GNKA.LD.QRQ.TQE..Q.LA.Q.KV.YME.SAKIRMN...A
Retrocopy FQRQILLRVKDHGEFPMIFMGNKAALDNQRQETQEK-QHLAQQCKVIYMEVSAKIRMNAEGA

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	3.87 RPM
SRP007412_cerebellum	0.00 RPM	4.50 RPM
SRP007412_heart	0.00 RPM	6.86 RPM
SRP007412_kidney	0.03 RPM	15.55 RPM
SRP007412_liver	0.24 RPM	13.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3043 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3043 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1604

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002367	1 retrocopy	retro_amel_947,
Bos taurus	ENSBTAG00000011905	1 retrocopy	retro_btau_1295,
Choloepus hoffmanni	ENSCHOG00000003135	7 retrocopies	retro_chof_111, retro_chof_1639, retro_chof_2065, retro_chof_2644, retro_chof_2706, retro_chof_389, retro_chof_521,
Dasypus novemcinctus	ENSDNOG00000011828	6 retrocopies	retro_dnov_124, retro_dnov_1458, retro_dnov_1708, retro_dnov_1779, retro_dnov_2331, retro_dnov_988,
Erinaceus europaeus	ENSEEUG00000000240	1 retrocopy	retro_eeur_531,
Felis catus	ENSFCAG00000009578	1 retrocopy	retro_fcat_386,
Homo sapiens	ENSG00000133818	1 retrocopy	retro_hsap_390,
Gorilla gorilla	ENSGGOG00000004759	1 retrocopy	retro_ggor_1813,
Myotis lucifugus	ENSMLUG00000007005	1 retrocopy	retro_mluc_1264,
Macaca mulatta	ENSMMUG00000000664	2 retrocopies	retro_mmul_1604, retro_mmul_965,
Monodelphis domestica	ENSMODG00000028397	2 retrocopies	retro_mdom_1254, retro_mdom_577,
Oryctolagus cuniculus	ENSOCUG00000011362	1 retrocopy	retro_ocun_1645,
Otolemur garnettii	ENSOGAG00000027655	1 retrocopy	retro_ogar_1081,
Ochotona princeps	ENSOPRG00000005967	1 retrocopy	retro_opri_2,
Pongo abelii	ENSPPYG00000025912	1 retrocopy	retro_pabe_3043 ,
Pan troglodytes	ENSPTRG00000003383	2 retrocopies	retro_ptro_1747, retro_ptro_301,
Rattus norvegicus	ENSRNOG00000012258	1 retrocopy	retro_rnor_750,
Ictidomys tridecemlineatus	ENSSTOG00000022169	1 retrocopy	retro_itri_1457,
Tupaia belangeri	ENSTBEG00000001292	1 retrocopy	retro_tbel_3234,
Tursiops truncatus	ENSTTRG00000010419	1 retrocopy	retro_ttru_1218,
Vicugna pacos	ENSVPAG00000008814	1 retrocopy	retro_vpac_165,