RetrogeneDB ID: retro_ptro_407

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:8720398..8721076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSPTRG00000019711
• Aliases: None
• Description: None

Sequence

>retro_ptro_407
GGTGGGACCTTGAGCACTCATCGGGTCACCTTCGAGGTGGACAAGAATGAGAACATCACCCATCACTGTGGTGAAGGGCA
TTGAGCTTTCAGAAAATGTGATTGATTGAATGAAGGAATCCTCTCCATCTGGTTCAAAGTCTCAGTGGTATTCTGATGCT
TATGATGCCTTGGTTTCTGATGAAGAATTGAAAAGAAGAGTAGCTGAGGAGCTAACATTGGAACAAGCCAAGAAACAAAC
TGAAGATCAGAAACGACTAAAGCAAGCCACAGAGCTGGAGAGAGAGAGGGCTGCTGCCAATGGGCAGTTAACCAGAGCCA
TCCCTCGAGAGAAGGTATCAAGCCAGGAGGAAGGCACTAAGGCAATGCACCTGGCTAGGTGGCTGGAAGAGAAAGGCCGA
GTGCTAAAGAAGCAGGTTGCATTCTGCAAAGTGGAGCTGGCTAGACTGGAGGAGAGGAGCTCAGAGTTCTACAAAGTCAC
CACTGAACAATATCAGAAAATTGCTGAAGAGGTGGAAGCACGGTTCAAGTGTATGAGTCTCATCCAGTCTATGCTGACCT
CCAGGCCAAAATTCTTCAGTGTTACTACGAGAACACCCACCAGACCTTCAAATGCTCCACTCTGGCCAGCCGGTATATGC
CCTATGTCAATCATGCCAAACAGAGCATGCTTGAGAAA

Alignment

ORF - retro_ptro_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.39 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGTTSTRRVTFEA--DEN-ENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAE
          GGT.ST.RVTFE....EN...ITVVKGI.LSENVID.MKESSPSGSKSQ.YS.AY.A.VSDEELKRRVAE
Retrocopy GGTLSTHRVTFEVDKNEN>SPITVVKGIELSENVID*MKESSPSGSKSQWYSDAYDALVSDEELKRRVAE

Parental  ELALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQD
          EL.LEQAKK..EDQKRLKQA.EL.RERAAAN.QLTRAI.RE..SS.EE..KA.HLAR.LEEK.RVLKKQ.
Retrocopy ELTLEQAKKQTEDQKRLKQATELERERAAANGQLTRAIPREKVSSQEEGTKAMHLARWLEEKGRVLKKQV

Parental  AFYKEQLARLEERSSEFYRVTTEQYQKAAEEVEAKFK-RYESHPVCADLQAKILQCYRENTHQTLKCSAL
          AF.K..LARLEERSSEFY.VTTEQYQK.AEEVEA.FK..YESHPV.ADLQAKILQCY.ENTHQT.KCS.L
Retrocopy AFCKVELARLEERSSEFYKVTTEQYQKIAEEVEARFK<VYESHPVYADLQAKILQCYYENTHQTFKCSTL

Parental  ATQYMHCVNHAKQSMLEK
          A..YM..VNHAKQSMLEK
Retrocopy ASRYMPYVNHAKQSMLEK

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	16.14 RPM
SRP007412_cerebellum	0.00 RPM	13.19 RPM
SRP007412_heart	0.00 RPM	62.43 RPM
SRP007412_kidney	0.00 RPM	38.42 RPM
SRP007412_liver	0.00 RPM	25.14 RPM
SRP007412_testis	0.00 RPM	13.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_407 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_407 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_542
Pongo abelii	retro_pabe_501

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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,