RetrogeneDB ID: retro_pabe_1166

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:44354944..44355491(-)
• 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_1166
ATGAGTGCTGCCAGAGAGTCTCACCTGCATGGGGTGAAGTGTTCAGCCTCCACAGATGACGATCTGGGATCTAGCAATTG
GGAGGCAGCAGACTTGGGTAATGAAGAGAAAAAACAAAAGTTCTTGAGACTTATGGGTGTAGGAAAGAAAAAACATACTG
GTCGTCTTATTATAGGAGATCGCAAATCAACATCACTCCTGAACGGGGGAAGAAGACAAGAAAATTAATGAAGAACTGGA
GACTCAATATCAGCAAAGTATGGACGGTAAATTATCAGGAAGATATCGGCGACATTGTGGACTTGGCTTCAATGAGGTAG
AAGATCATGATGGAGAAGGTGATGTGGCTGGAGTTGATGATGACGATGATGATGATTCACCTGATCCTGAAAGTCTAGAT
GATTCTGAAAGCGATTCAGAGTCAGAGAAAGAAGAATCTGCTGAAGAACTCCAAGCTGCTGAGCACCCTGATGAAATGGA
GGATCCCAAAAACAAAAAAGATGCAAAAAGCAATTATAAAATGATGTTTGTGAAATCCAGTGGTTCA

Alignment

ORF - retro_pabe_1166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSAARESHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKF-LRLMGAGK-KEHIDCLVLGDHKSTFHFR
          MSAARESH.HGVK.SAS.DDDLGSSNWEAADLGNEE.KQKF.L...G..K....I....L.......H..
Retrocopy MSAARESHLHGVKCSASTDDDLGSSNWEAADLGNEEKKQKF<LETYGCRK<RKNILVVLL*EIANQHHS*

Parental  TGEEDKKINEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGDDDDDDDDSPDPESPDDSES
          TGEEDKKINEELE.QYQQSMD.KLSGRYRRHCGLGF.EVEDHDGEGDVAG.DDDDDDDSPDPES.DDSES
Retrocopy TGEEDKKINEELETQYQQSMDGKLSGRYRRHCGLGFNEVEDHDGEGDVAGVDDDDDDDSPDPESLDDSES

Parental  DSESEKEESAEELQAAEHPDEVEDPKNKKDAKSNYKMMFVKSSGS
          DSESEKEESAEELQAAEHPDE.ED.............MFVKSSGS
Retrocopy DSESEKEESAEELQAAEHPDEMEDXXXXXXXXXXXXXMFVKSSGS

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	0.61 RPM	71.93 RPM
SRP007412_cerebellum	0.49 RPM	39.16 RPM
SRP007412_heart	0.42 RPM	38.56 RPM
SRP007412_kidney	0.56 RPM	56.05 RPM
SRP007412_liver	0.31 RPM	36.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1166 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1166 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1408

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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,