RetrogeneDB ID: retro_pabe_501

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:8993646..8994324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSPPYG00000025827
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:HGNC Symbol;Acc:21906]

Sequence

>retro_pabe_501
GGTGGGACCTTGAGCACTCATCGGGTCACCTTCGAGGTGGACAAGAATGAGAACATCACCCATCAACGTGGTGAAGGGCA
TTGGGCTTTCAGAAAATGTGATTGATTGAATGAAGGAATCCTCTCCATCTGGTTCAAAGTCTCAGCGGTATTCTGGTGCT
TATGATGCCTTGGTTTCTGATGAAGAATTGAAAAGAAGAGTAGCTGAGGAGCTAACATTGGAACACGCCAAGAAACAAAC
TGAAGATCAGAAACGACTAAAGCAAGCCACAGAGCTGGAGAGAGAGAGGGCTTCTGCCAATGGGCAGTTAATCAGAGCCA
TCCCTTGAGAGAGGGTATCAAGCCAGGAGGAAGGCACTAAGGCAATGCACCTGGCTAGGCAGCTGGAAGAGAAAGACCGA
GTGCTAAAGAAGCAGGTTGCATTCTGCAAAGTGGAGCTGGATAGACTGGAGGAGAGGAGCTCAGAGTTCTACAAAGTCAC
CACTGAACAATATCAGAAAATTGCTGAAGAGGTGGAAGCACGGTTCAAGTGTATGAGTCTCATCCAGTCTACGCTGACCT
GCAGGCCAAAATTCTTCAGCGTTACTACGAGAACACCCACCAGACCTTCAAACGCTCCACTCTGGCCAGCCGGTATATGC
ACTATGTCAATCATGCCAAACAGAGCATGCTTGAGAAA

Alignment

ORF - retro_pabe_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.07 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGTTSTRRVTFEA--DEN-ENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAE
          GGT.ST.RVTFE....EN...I.VVKGI.LSENVID.MKESSPSGSKSQRYSGAY.A.VSDEELKRRVAE
Retrocopy GGTLSTHRVTFEVDKNEN>SPINVVKGIGLSENVID*MKESSPSGSKSQRYSGAYDALVSDEELKRRVAE

Parental  ELALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQD
          EL.LE.AKK..EDQKRLKQA.EL.RERA.AN.QL.RAI..ER.SS.EE..KA.HLARQLEEKDRVLKKQ.
Retrocopy ELTLEHAKKQTEDQKRLKQATELERERASANGQLIRAIP*ERVSSQEEGTKAMHLARQLEEKDRVLKKQV

Parental  AFYKEQLARLEERSSEFYRVTTEQYQKAAEEVEAKFK-RYESHPVCADLQARILQCYRENTHQTLKCSAL
          AF.K..L.RLEERSSEFY.VTTEQYQK.AEEVEA.FK..YESHPV.ADLQA.ILQ.Y.ENTHQT.K.S.L
Retrocopy AFCKVELDRLEERSSEFYKVTTEQYQKIAEEVEARFK<VYESHPVYADLQAKILQRYYENTHQTFKRSTL

Parental  ATQYMHCVNHAKQSMLEK
          A..YMH.VNHAKQSMLEK
Retrocopy ASRYMHYVNHAKQSMLEK

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	10.56 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.00 RPM	26.28 RPM
SRP007412_kidney	0.00 RPM	13.13 RPM
SRP007412_liver	0.00 RPM	8.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_501 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_501 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_542
Pan troglodytes	retro_ptro_407

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501 ,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,