RetrogeneDB ID: retro_ptro_2096

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:141192776..141193614(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSPTRG00000020298
• Aliases: None
• Description: Armadillo repeat-containing protein 1 [Source:UniProtKB/TrEMBL;Acc:H2QW84]

Sequence

>retro_ptro_2096
ATGAATTCTTCCACCTCCACCATGAGTGAAGAGTCTGATACTCTATCGGTAGTTAACCAGTTAGGGGATATAGCAGCAGA
TCCATTAAACAGAAGAGCTGTAGTCCAGGATCAGGGATGTCTGCCTTGCCTTATTTTATTTATGGACCACCCTAACCCTC
CAGTCCATTTGGCTTTGCTCGCTCTTCGATACTTGGGAGAACACCGTGCAAACAGAGAAAAGATGAAAGGAGAACTGGGT
ATGATGTTGAGCCTACAAAATGTTATACAGAAAACTGCAACTCTGGGAGAAACAAAACTTCTGGCCTCTGAAATCTATGA
CATACTTCAGTCCTCCAATAAGGCAGATGGTGATAGTTTCAATGAAATGAATTCATATTGAAGGAAAGCTCAGTTTTTTC
TGGGAACTGCAAACAAACGTGCCAAAACAGTGGTTTTGCATATAGACGGCCTTGATGATACGTCTTCGAGAAATCTATAT
GAAGAGGCTTTGTTAAAAATTAAAGGTATTATTAGCTTTACTTTTCAAATGGCTGTTCAAAGGCGTGGTGTGAATCCGTT
CAGATTTGAAAGCTGAGGCTTTCGCATCAGCGAGAGCATCAACCAAGGTTATGAAAGCTCCGTAAGTTGTGAAAAGTGAA
AGTGGAGAAGAGATGCTGGTCCCATTCCAAGACCTTCCTGTGGTAGAACAGAACACAGGGCTACCTGACTACGTGTCTGA
AGATAAGAGTCCCACAAATGAACAGTACAAGGTGGTGTCCTGGGTCAGCTCATACCCAGTGGGTGGAACTAGCTGGCTGA
GCACAGCTGCAAACTTTTTATCCAGATCGTTTTATTGG

Alignment

ORF - retro_ptro_2096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSTSTMSEEPDALSVVNQLRDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAECR
          MNSSTSTMSEE.D.LSVVNQL.D.AADPLNRRA.VQDQGCLP.LILFMDHPNPPV.H.ALLALRYL.E.R
Retrocopy MNSSTSTMSEESDTLSVVNQLGDIAADPLNRRAVVQDQGCLPCLILFMDHPNPPV-HLALLALRYLGEHR

Parental  ANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKAQFFLGTTNK
          ANREKMKGELGMMLSLQNVIQKT.T.GETKLLASEIYDILQSSN.ADGDSFNEMNS..RKAQFFLGT.NK
Retrocopy ANREKMKGELGMMLSLQNVIQKTATLGETKLLASEIYDILQSSNKADGDSFNEMNSY*RKAQFFLGTANK

Parental  RAKTVVLHIDGLDDTSRRNLCEEALLKI-KGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQ
          RAKTVVLHIDGLDDTS.RNL.EEALLKI.K......F.......VV.IRSDLKAEA.ASA.ASTKVMKA.
Retrocopy RAKTVVLHIDGLDDTSSRNLYEEALLKI>KVLLALLFKWLFKG-VV*IRSDLKAEAFASARASTKVMKAP

Parental  QVVKSESGEEMLVPFQDTPVEVEQNTELPDYLPEDESPTKEQDKAVSRVGSHPEGGASWLSTAANFLSRS
          .VVKSESGEEMLVPFQD.PV.VEQNT.LPDY..ED.SPT.EQ.K.VS.V.S.P.GG.SWLSTAANFLSRS
Retrocopy *VVKSESGEEMLVPFQDLPV-VEQNTGLPDYVSEDKSPTNEQYKVVSWVSSYPVGGTSWLSTAANFLSRS

Parental  FYW
          FYW
Retrocopy FYW

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	26.31 RPM
SRP007412_cerebellum	0.00 RPM	27.85 RPM
SRP007412_heart	0.00 RPM	16.53 RPM
SRP007412_kidney	0.00 RPM	19.33 RPM
SRP007412_liver	0.00 RPM	11.39 RPM
SRP007412_testis	0.00 RPM	14.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2096 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2096 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096 ,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,