RetrogeneDB ID: retro_ggor_2129

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:148503752..148504590(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSGGOG00000022803
• Aliases: None
• Description: Armadillo repeat-containing protein 1 [Source:UniProtKB/TrEMBL;Acc:G3RPG2]

Sequence

>retro_ggor_2129
ATGAATTCTTCCACCTCCACCATGAGTGAAGAGTCTGATACTCCATCGGTAGTTAACCAGTTAGGGGATATAGCAGCAGA
TCCATTAAACAGAAGAGCTGTAGTCCAGGATCAGGGATGTCTGCCTTGCCTTATTTTATTTATGGACCACCCCAACCCTC
CAGTCCATTTGGCTTTGCTCACTCTTCGCTACTTGGGAGAATGCCGTGCAAACAGAGAAAAGATGAAAGGAGAACTGGGT
ATGATGTTGAGCCTACAAAATGTTATATAGAAAACTGCAACTCTGGGAGAAACAAAACTTCTGGCCTCTGAAATCTATGA
CATACTTCAGTCCTCCAATAAGGCAGATGGTGATAGTTTCAATGAAATGAATTCATATTGAAAGAAAGCTCAGTTTTTTC
TGGGAACTACAAACAAACGTGCCAAAACAGTGGTTTTGCATATAGACGGCCTTGATGATACGTCTTCGAGAAATCTATGT
GAAGAGGCTTTGTTAAAAATTAAAGGTGTTATTAGCTTTACTTTTCAAATGGCTGTTCAAAGGCGTGGTGTGAATCCATT
CAGATTTGAAAGCTGAGGCTTTGGCATCAGCGAGAGCATCAACCAAGGTTATGAAAGCTCCGTAAGTTGTGAAAAGTGAA
AGTGGAGAAGAGATGCTGGTCCCATTCCAAGACCTTCCTGTGGTAGAACAGAACACAGAGCTACCTGACTACTTGTCTGA
AGATGAGAGTCCCACAAATGAACAGTACAAGGTGGTGTCCTGGGTCAGCTCACACCCAGTGGGTCGAACTAGCTGGCTGA
GCATAGCTACAAACTTTTTATCCAGATCGTTTTATTGG

Alignment

ORF - retro_ggor_2129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSTSTMSEEPDALSVVNQLRDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAECR
          MNSSTSTMSEE.D..SVVNQL.D.AADPLNRRA.VQDQGCLP.LILFMDHPNPPV.H.ALL.LRYL.ECR
Retrocopy MNSSTSTMSEESDTPSVVNQLGDIAADPLNRRAVVQDQGCLPCLILFMDHPNPPV-HLALLTLRYLGECR

Parental  ANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKAQFFLGTTNK
          ANREKMKGELGMMLSLQNVI.KT.T.GETKLLASEIYDILQSSN.ADGDSFNEMNS...KAQFFLGTTNK
Retrocopy ANREKMKGELGMMLSLQNVI*KTATLGETKLLASEIYDILQSSNKADGDSFNEMNSY*KKAQFFLGTTNK

Parental  RAKTVVLHIDGLDDTSRRNLCEEALLKI-KGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQ
          RAKTVVLHIDGLDDTS.RNLCEEALLKI.K......F.......VV.I.SDLKAEALASA.ASTKVMKA.
Retrocopy RAKTVVLHIDGLDDTSSRNLCEEALLKI>KVLLALLFKWLFKG-VV*IHSDLKAEALASARASTKVMKAP

Parental  QVVKSESGEEMLVPFQDTPVEVEQNTELPDYLPEDESPTKEQDKAVSRVGSHPEGGASWLSTAANFLSRS
          .VVKSESGEEMLVPFQD.PV.VEQNTELPDYL.EDESPT.EQ.K.VS.V.SHP.G..SWLS.A.NFLSRS
Retrocopy *VVKSESGEEMLVPFQDLPV-VEQNTELPDYLSEDESPTNEQYKVVSWVSSHPVGRTSWLSIATNFLSRS

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	0.05 RPM	11.60 RPM
SRP007412_cerebellum	0.00 RPM	10.76 RPM
SRP007412_heart	0.00 RPM	1.94 RPM
SRP007412_kidney	0.04 RPM	14.52 RPM
SRP007412_liver	0.00 RPM	10.26 RPM
SRP007412_testis	0.10 RPM	11.60 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2129 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,