RetrogeneDB ID: retro_pabe_2307

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:55247047..55247469(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSPPYG00000004599
• Aliases: None
• Description: chromobox homolog 5 [Source:HGNC Symbol;Acc:1555]

Sequence

>retro_pabe_2307
ATGGGAAAGAAAACCAAGCACACAGCTGACAGTTCATCAGAGAATGAAGAGGAGTACACTGTGGAGAAGGTGCTAGACAG
GCATGTAGTTAAGGGGCAAGTGGATTATCTACTGAAGTAGAAAGGCTTTTCTGAGGAGCACAATACTTGGGAATCTGAGA
AAAACTTGGATTGCCTTTAGCTCATTTCTTAGTTTACAAAAAAGTTTAAGATGATGAAGGAGGGTTAAAATAACAAGCCT
GGGGAGAAGTCACAAAGTAGCAAGGAAATCCAGTTTCTCAAACTGTGCTGACAGTATCAAGTCCAAAAAAGAGAACAGAG
TGATGATATTGCTTGGGGCTTCGAGATAAGGCTAGAACCAGAAAAGATCATTGGGGCAACAGATTCCTGTGGCGATTTAT
GTTTTTAATGAAATGGAAAGAC

Alignment

ORF - retro_pabe_2307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKY
          MGKKTK.TADSSS.E.EEEY.VEKVLDR.VVKGQV.YLLK.KGFSEEHNTWE.EKNLDC..LIS.F.KK.
Retrocopy MGKKTKHTADSSS-ENEEEYTVEKVLDRHVVKGQVDYLLK*KGFSEEHNTWESEKNLDCL*LIS*FTKKF

Parental  KKMKEGENNKPREKSESNKRKSSFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDL-MFL
          K.MKEG.NNKP.EKS.S.K....F..........K.......IA.GFE..LEPEKIIGATDSCGDL.MFL
Retrocopy KMMKEG*NNKPGEKSQSSK-EIQFLKLC*QYQVQKREQSDD-IAWGFEIRLEPEKIIGATDSCGDL<MFL

Parental  MKWKD
          MKWKD
Retrocopy MKWKD

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	10.84 RPM
SRP007412_cerebellum	0.00 RPM	9.61 RPM
SRP007412_heart	0.06 RPM	7.38 RPM
SRP007412_kidney	0.03 RPM	9.28 RPM
SRP007412_liver	0.00 RPM	3.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2307 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2307 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2811
Pan troglodytes	retro_ptro_1905
Gorilla gorilla	retro_ggor_1955

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307 ,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Pongo abelii	ENSPPYG00000017714	10 retrocopies	retro_pabe_2112, retro_pabe_2243, retro_pabe_2724, retro_pabe_2770, retro_pabe_2997, retro_pabe_3608, retro_pabe_758, retro_pabe_786, retro_pabe_892, retro_pabe_951,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,