RetrogeneDB ID: retro_pabe_3658

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:71787545..71787980(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSPPYG00000013423
• Aliases: CNBP, ZNF9
• Description: Cellular nucleic acid-binding protein [Source:UniProtKB/Swiss-Prot;Acc:Q5R5R5]

Sequence

>retro_pabe_3658
GGGCGAGGAGGTGGAGGCCATGGCAGAGGTTCTCAATGTGGTTCCACCACCCTATCTTACACCTGTTACTGCTGTGGTGA
GTCCAGTCGTCATGCTAAGAACTGTGTCCTTCTCGGAAACATCTGCTACAACTGTGGGAGAAGCGGCCACATCGCCAAAG
ACTGTAAGGAACCTAAACGGGAGAGACACCAACACTGTTATACCTGCGGCAGACTAGGACATCTGGCTCGTGACTGTGAT
CGTCAGAAAGAGCAGAAATGCTACTCTTGCGGCAAACTTGGGCACATTCAGAAAGACTGCGCCCAGGTCAAGTGTTACCG
ATGCGGCGAGATTGGCCACGTGGCCATTAATTGCAGCAAGGCGAGCCAGGTCAACTGCTACCGCTGCGGCAAATCCGGAC
ATCTAGCCAGGGAATGTCCCAGTGAGGTTACCGCT

Alignment

ORF - retro_pabe_3658 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.03 %
• Parental protein coverage: 81.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCG
          GRGG....RG.Q..S..L...CY.CGES...AK.C.L....CYNCGR.GHIAKDCKEPKRER.Q.CY.CG
Retrocopy GRGGGGHGRGSQCGSTTLSYTCYCCGESSRHAKNCVLLGNICYNCGRSGHIAKDCKEPKRERHQHCYTCG

Parental  KPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECT
          ..GHLARDCD...EQKCYSCG..GHIQKDC..VKCYRCGE.GHVAINCSK.S.VNCYRCG.SGHLAREC.
Retrocopy RLGHLARDCDRQKEQKCYSCGKLGHIQKDCAQVKCYRCGEIGHVAINCSKASQVNCYRCGKSGHLARECP

Parental  IEATA
          .E.TA
Retrocopy SEVTA

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	126.01 RPM
SRP007412_cerebellum	0.00 RPM	197.85 RPM
SRP007412_heart	0.00 RPM	221.80 RPM
SRP007412_kidney	0.00 RPM	146.18 RPM
SRP007412_liver	0.00 RPM	174.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3658 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3658 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_50
Equus caballus	retro_ecab_1072

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015334	2 retrocopies	retro_amel_1285, retro_amel_1773,
Canis familiaris	ENSCAFG00000004320	2 retrocopies	retro_cfam_1272, retro_cfam_23,
Cavia porcellus	ENSCPOG00000012816	2 retrocopies	retro_cpor_424, retro_cpor_94,
Dipodomys ordii	ENSDORG00000002919	1 retrocopy	retro_dord_569,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Homo sapiens	ENSG00000169714	1 retrocopy	retro_hsap_50,
Gorilla gorilla	ENSGGOG00000010085	1 retrocopy	retro_ggor_2926,
Macropus eugenii	ENSMEUG00000011699	1 retrocopy	retro_meug_55,
Myotis lucifugus	ENSMLUG00000012554	1 retrocopy	retro_mluc_141,
Macaca mulatta	ENSMMUG00000011585	1 retrocopy	retro_mmul_2505,
Mustela putorius furo	ENSMPUG00000017315	3 retrocopies	retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus	ENSMUSG00000030057	1 retrocopy	retro_mmus_230,
Nomascus leucogenys	ENSNLEG00000014482	1 retrocopy	retro_nleu_1986,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Ochotona princeps	ENSOPRG00000005487	5 retrocopies	retro_opri_139, retro_opri_49, retro_opri_496, retro_opri_566, retro_opri_965,
Pongo abelii	ENSPPYG00000013423	1 retrocopy	retro_pabe_3658 ,
Pan troglodytes	ENSPTRG00000015369	1 retrocopy	retro_ptro_3131,
Rattus norvegicus	ENSRNOG00000010239	2 retrocopies	retro_rnor_207, retro_rnor_727,
Ictidomys tridecemlineatus	ENSSTOG00000000173	1 retrocopy	retro_itri_113,
Tarsius syrichta	ENSTSYG00000004344	1 retrocopy	retro_tsyr_1889,
Vicugna pacos	ENSVPAG00000007138	1 retrocopy	retro_vpac_548,