RetrogeneDB ID: retro_pabe_945

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:79301859..79302382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSPPYG00000017619
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_pabe_945
ATGCCCGCAAATAAGCCCAAGGGTCAGAATAATTTGGCCTTACACAAAGTCATCACGGTGGGCAGTGCCGGTGTGGGCAA
GGCAGCTCTGACTCTACAGTTCATGTACGATGAGTTTGTGGAGGACTATGAGCTTATCAAATAAGGCACCTATCGGAAGA
AAGTAGTACTGGATGGCGAGGAAGTACAGATCGATATCGTAGAAACAGCTGGGCAGGAGGGCTATGCTGCAATTAGGGAC
AACTATTTCCGAAGCAGAGAGGGGTTTCTGTGTCTTCTCTATTACAGAAATGGAATCCTTTGCAGCTACAGCTGACTTCA
GGGAGCAGATTTTAAGAGTAAAAGAAGATGAGAATGTTTCATTTCTACTGGTTGGTAACAAATCAAATTTAGAAGATAAA
AGGCCGGTTTCTGTAAAAGAGGCAAAAAACAGAGCTGACCAGTGGAATGTTAACTATGTGGAAACATCTGCTAAAACACG
AGCTAATGTTGACAGGGTATTTTTTGATTTAATGAGAGAAATT

Alignment

ORF - retro_pabe_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 84.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTA
          M.ANKPKGQN.LALHKVI.VGS.GVGK.ALTLQFMYDEFVEDYE..K...YRKKVVLDGEEVQIDI..TA
Retrocopy MPANKPKGQNNLALHKVITVGSAGVGKAALTLQFMYDEFVEDYELIK*GTYRKKVVLDGEEVQIDIVETA

Parental  GQEDYAAIRDNYFRSGE-GFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV
          GQE.YAAIRDNYFRS.E.GF.CVFSITEMESFAATADFREQILRVKEDENV.FLLVGNKS.LEDKR.VSV
Retrocopy GQEGYAAIRDNYFRSRE>GF-CVFSITEMESFAATADFREQILRVKEDENVSFLLVGNKSNLEDKRPVSV

Parental  EEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREI
          .EAKNRA.QWNVNYVETSAKTRANVD.VFFDLMREI
Retrocopy KEAKNRADQWNVNYVETSAKTRANVDRVFFDLMREI

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	15.20 RPM
SRP007412_cerebellum	0.00 RPM	12.16 RPM
SRP007412_heart	0.00 RPM	9.30 RPM
SRP007412_kidney	0.03 RPM	12.60 RPM
SRP007412_liver	0.00 RPM	11.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_945 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_945 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1136
Macaca mulatta	retro_mmul_882

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pongo abelii	ENSPPYG00000004369	1 retrocopy	retro_pabe_2870,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945 ,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,