RetrogeneDB ID: retro_pabe_2677

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:116535129..116535432(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMC1
• Ensembl ID: ENSPPYG00000014054
• Aliases: None
• Description: COX assembly mitochondrial protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28783]

Sequence

>retro_pabe_2677
GCCCAGCAGCAACTAAGATATGTCGAAAAAGATGTTCTGATGCCTAACATAATGAGAAAAATGGCCAGAGAGAGGTATTC
TGAAAAAGTTCAAGATTTTACCAAGTGTTGCAAGAACTCTAGAATCCTTATGGTGGTAAAATACTGGAAATACAATTCTG
CATTGAAAGACTGTCTTAACTGCTTACTATAATGATCCAGTCTTTTACAAAGAATACAAAATGGAATACCTGAAGGAATG
TAAGAACTCAGAAAAACTGGAATTTCTACCAAGTTAAAGCTACAGAAGCTTCCCATAAGCATG

Alignment

ORF - retro_pabe_2677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 95.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADQHLRHVEKDVLIPKIMREKAKERCSEQVQDFTKCCKNSGVLMVVKCRKENSALKEC-LTAYYNDPAFY
          A.Q.LR.VEKDVL.P.IMR..A.ER.SE.VQDFTKCCKNS..LMVVK..K.NSALK.C.LTAYYNDP.FY
Retrocopy AQQQLRYVEKDVLMPNIMRKMARERYSEKVQDFTKCCKNSRILMVVKYWKYNSALKDC>LTAYYNDPVFY

Parental  EECKMEYLKERE-EFRKTGIPAKKRLQKLPTSM
          .E.KMEYLKE...E.RKTGI..K..LQKLP.SM
Retrocopy KEYKMEYLKECK<ELRKTGISTKLKLQKLPISM

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	3.43 RPM
SRP007412_cerebellum	0.00 RPM	6.20 RPM
SRP007412_heart	0.00 RPM	5.39 RPM
SRP007412_kidney	0.00 RPM	5.34 RPM
SRP007412_liver	0.00 RPM	6.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2677 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2677 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3229
Pan troglodytes	retro_ptro_2181
Gorilla gorilla	retro_ggor_2196

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004272	2 retrocopies	retro_cjac_2600, retro_cjac_2653,
Dasypus novemcinctus	ENSDNOG00000018923	2 retrocopies	retro_dnov_111, retro_dnov_651,
Homo sapiens	ENSG00000187118	4 retrocopies	retro_hsap_1372, retro_hsap_1764, retro_hsap_3229, retro_hsap_984,
Gorilla gorilla	ENSGGOG00000012406	4 retrocopies	retro_ggor_1067, retro_ggor_2196, retro_ggor_2245, retro_ggor_786,
Microcebus murinus	ENSMICG00000011702	2 retrocopies	retro_mmur_366, retro_mmur_759,
Myotis lucifugus	ENSMLUG00000000044	2 retrocopies	retro_mluc_1063, retro_mluc_759,
Nomascus leucogenys	ENSNLEG00000004066	4 retrocopies	retro_nleu_1075, retro_nleu_2763, retro_nleu_2830, retro_nleu_949,
Oryctolagus cuniculus	ENSOCUG00000012793	2 retrocopies	retro_ocun_1592, retro_ocun_1637,
Ochotona princeps	ENSOPRG00000009474	1 retrocopy	retro_opri_463,
Pongo abelii	ENSPPYG00000014054	4 retrocopies	retro_pabe_1139, retro_pabe_1533, retro_pabe_2677 , retro_pabe_833,
Pan troglodytes	ENSPTRG00000014706	4 retrocopies	retro_ptro_1207, retro_ptro_2181, retro_ptro_763, retro_ptro_942,
Rattus norvegicus	ENSRNOG00000010149	1 retrocopy	retro_rnor_914,
Sorex araneus	ENSSARG00000001629	1 retrocopy	retro_sara_186,
Tupaia belangeri	ENSTBEG00000002573	4 retrocopies	retro_tbel_3026, retro_tbel_3858, retro_tbel_4018, retro_tbel_4214,
Tarsius syrichta	ENSTSYG00000011371	2 retrocopies	retro_tsyr_1764, retro_tsyr_178,