RetrogeneDB ID: retro_ptro_1564

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:106677992..106678635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6ORF106
• Ensembl ID: ENSPTRG00000018068
• Aliases: None
• Description: Chromosome 6 open reading frame 106 [Source:UniProtKB/TrEMBL;Acc:K7DPL6]

Sequence

>retro_ptro_1564
AACCTACAAGCAGCAATTGGTGCCTCTTATGCCTTTGAGAGCTCAAACATCAGTGTGCCCTCTGTGTCCTTTGTTGAAGA
TGTCACCCTAGAGGAAGGGTAGTCAATACCTCCTGATACTCAGTTTGTAAAAACTTGGTGGATCCAGAATTCTGCGGCAG
AGGCCTGGCCTCCAGGGGTTTGTCCTAAATATGTCAGGGGAGACCAAGTTGGACATGTGAACATGCTGATGGTGAGATTG
CTAGAGCCGCAAGAGATTACAGATGTTATTGTCCAGATGCGCAGCCCCAGCAGAGCAGGAACGTATCAGGGACGGTGACG
GATGTGCACTGCTACAGGACTCTACTATGGAGATGTCATCTGGGTGATTCTCAGTGTGGAGGTGGGTGGACTTTGAGAAG
TAACACAGCAGCTGTCATCTTTTGAAACGGAGTTCAACACAGCCGCATAGCAAGGTAGAAGGAAACTTCAACCCTTTTGC
CTCTCCCCAAAAGAACCAACAATCAGATGAAAACAACTTACAAGACCCTGGGGGTTCCGAGTTCTACTCGATCAGCAAAA
ACACATGGGCTCCTGCTCCTGACCAAGCTGAGCAAGACCAGAGCAGACTGTCACAGAACTCTGTAAATCTGTCTCCCAGC
AGT

Alignment

ORF - retro_ptro_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 87.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFVKTWRIQNSGAEAWPPGVCLKYVGGDQF
          NLQAAIGA.Y.FES.NISVPS.SFVEDVT..EG.SIPPDTQFVKTW.IQNS.AEAWPPGVC.KYV.GDQ.
Retrocopy NLQAAIGASYAFESSNISVPSVSFVEDVTLEEG*SIPPDTQFVKTWWIQNSAAEAWPPGVCPKYVRGDQV

Parental  GHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLSS
          GHVNM.MVR.LEPQEI.DV.VQM.SPSRAG.YQG..RMCTATGLYYGDVIWVILSVEVGGL..VTQQLSS
Retrocopy GHVNMLMVRLLEPQEITDVIVQMRSPSRAGTYQGR*RMCTATGLYYGDVIWVILSVEVGGL*EVTQQLSS

Parental  FETEFNT---QPHRKVEGNFNPFASPQKNRQSDENNLKDPGG-SEFDSISKNTWAPAPDTWAPAPDQTEQ
          FETEFNT...Q..RK......PF....K........L..P.G.SEF.SISKNTWAPAPD..........Q
Retrocopy FETEFNTAA*QGRRKLQ----PFCLSPKEPTIR*KQLTRPWG>SEFYSISKNTWAPAPDQAEQDQSRLSQ

Parental  DQNRLSQNS
          ....LS..S
Retrocopy NSVNLSPSS

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	0.45 RPM	76.40 RPM
SRP007412_cerebellum	2.26 RPM	151.53 RPM
SRP007412_heart	0.93 RPM	84.26 RPM
SRP007412_kidney	1.31 RPM	73.56 RPM
SRP007412_liver	0.95 RPM	68.02 RPM
SRP007412_testis	1.90 RPM	110.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1564 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1564 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2137

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564 ,