RetrogeneDB ID: retro_pabe_2090

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:123331509..123331869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX20
• Ensembl ID: ENSPPYG00000000053
• Aliases: None
• Description: COX20 cytochrome C oxidase assembly factor [Source:HGNC Symbol;Acc:26970]

Sequence

>retro_pabe_2090
ATGGCCCCCGCTCCGGAGCCCTGCGAGCCCGCGAAGGGGAAGCTCTTTAAGCTCCTAGGCATTTCAGTTGTTGAAAATAT
TCCCTGTGCCCGGGATTCAATATTGTATGCTTCATTAGGATCTGTTGTGGCTGGCTTTGGACATTTTTTTTTGTTAACTA
GTAGAATTTGAAAATCATGTGATGTTGGAGTAGGAGGATTTATCTTGGTGACTTTGGGATGCTGGTTTCATTGTAGGTAT
AATTATGCAAAGCAAAGAATCCAGGAAAGAATTGCCAGAGAAGGAATTAAAAATAAGATGTTACACGAAAGTACCCACCT
TGATCCTGAAAGAAAAGAAACCAAGGGCAACAGCAGCAAT

Alignment

ORF - retro_pabe_2090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPEPGEPKERKSLKLLGFLDVENTPCARHSILYGSLGSVVAGFGHFL-FTSRIRRSCDVGVGGFILV
          MA.APEP.EP...K..KLLG...VEN.PCAR.SILY.SLGSVVAGFG.....TSRI..SCDVGVGGFILV
Retrocopy MAPAPEPCEPAKGKLFKLLGISVVENIPCARDSILYASLGSVVAGFGXXXXLTSRI*KSCDVGVGGFILV

Parental  TLGCWFHCRYNYAKQRIQERIAREEIKKKILYEGTHLDPERKH-NGSSSN
          TLGCWFHCRYNYAKQRIQERIARE.IK.K.L.E.THLDPERK...G.SSN
Retrocopy TLGCWFHCRYNYAKQRIQERIAREGIKNKMLHESTHLDPERKETKGNSSN

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	19.74 RPM
SRP007412_cerebellum	0.00 RPM	43.90 RPM
SRP007412_heart	0.12 RPM	25.83 RPM
SRP007412_kidney	0.10 RPM	37.89 RPM
SRP007412_liver	0.15 RPM	22.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2090 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001381	4 retrocopies	retro_chof_1820, retro_chof_207, retro_chof_299, retro_chof_825,
Erinaceus europaeus	ENSEEUG00000012147	1 retrocopy	retro_eeur_104,
Homo sapiens	ENSG00000203667	1 retrocopy	retro_hsap_587,
Myotis lucifugus	ENSMLUG00000026132	7 retrocopies	retro_mluc_1273, retro_mluc_1505, retro_mluc_1863, retro_mluc_1954, retro_mluc_2343, retro_mluc_792, retro_mluc_958,
Monodelphis domestica	ENSMODG00000024669	1 retrocopy	retro_mdom_2014,
Mus musculus	ENSMUSG00000026500	1 retrocopy	retro_mmus_2957,
Nomascus leucogenys	ENSNLEG00000004027	1 retrocopy	retro_nleu_2518,
Ochotona princeps	ENSOPRG00000004534	6 retrocopies	retro_opri_1072, retro_opri_287, retro_opri_31, retro_opri_585, retro_opri_676, retro_opri_720,
Pongo abelii	ENSPPYG00000000053	1 retrocopy	retro_pabe_2090 ,
Pteropus vampyrus	ENSPVAG00000002577	1 retrocopy	retro_pvam_945,
Rattus norvegicus	ENSRNOG00000004553	2 retrocopies	retro_rnor_1033, retro_rnor_2184,
Sorex araneus	ENSSARG00000004625	2 retrocopies	retro_sara_167, retro_sara_470,
Tupaia belangeri	ENSTBEG00000015272	4 retrocopies	retro_tbel_1186, retro_tbel_3207, retro_tbel_3838, retro_tbel_3926,
Tarsius syrichta	ENSTSYG00000005644	1 retrocopy	retro_tsyr_100,