RetrogeneDB ID: retro_pabe_3178

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:122038458..122038798(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf58
• Ensembl ID: ENSPPYG00000003458
• Aliases: None
• Description: small acidic protein [Source:RefSeq peptide;Acc:NP_001125161]

Sequence

>retro_pabe_3178
AGGGAGTCCTATCCTCACAGGGTGAAGTGTTCAGTCTTCACAGACAACAATCTTGGACCTAGCAATTAGTAGTTAGCAAA
CTTAGGTAATGAAGAAAGAAAGTAAACATTCTTTAGACATGGGTGTAGAAAAGAAAGAACATGCTGTCCGTCTTGTTACA
GGAGATCAAAAATCAACATCTTACTTCTGAAAAGGGGAAGAAGACAAGATAATTGATGAGGAACTGGATTTTCAATATCA
GCCAGGTGTCAGTAGTCAATTTTCAGGAAGTTACAGATGACACTGTGAACTTGGCTTTAGTAAAGTACATCATGATGAAG
CAGGTGATGTAGCTGGAGAG

Alignment

ORF - retro_pabe_3178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RESHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLRLMGAGKK-EHIDCLVLGDHKSTFHFRTGEED
          RES.PH.VK.S...D..LG.SN...A.LGNEERK..F.R..G..K..EH...LV.GD.KST..F..GEED
Retrocopy RESYPHRVKCSVFTDNNLGPSN**LANLGNEERK*TFFR-HGCRKE>EHAVRLVTGDQKSTSYF*KGEED

Parental  KKINEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGD
          K.I.EEL..QYQ....S..SG.YR.HC.LGFS.V..HD..GDVAG.
Retrocopy KIIDEELDFQYQPGVSSQFSGSYR*HCELGFSKVH-HDEAGDVAGE

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	71.93 RPM
SRP007412_cerebellum	0.00 RPM	39.16 RPM
SRP007412_heart	0.00 RPM	38.56 RPM
SRP007412_kidney	0.00 RPM	56.05 RPM
SRP007412_liver	0.00 RPM	36.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3178 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178 ,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,