RetrogeneDB ID: retro_ggor_2223

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:155759738..155760632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP46
• Ensembl ID: ENSGGOG00000017197
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G3RLX0]

Sequence

>retro_ggor_2223
ATCTGTACCATGAGTGCCAGTGCTTCGGCATTAGAGAAAGAGATTGGTCCAGAACAGTTTCCAGTGAATGAGCACTATTT
TGGATTAGTCAGTTTTGGGAATACCTGCTACTGCAATTCAGTTCTTCAAGCACTTTATTTTTGTCGTCCATTTCGGGAAA
CAGTTCTTGCATAGAAGAGTCAACCTAGGAAAAAGGAGAGCCTTCTTACATGCTTAGCAGATCTCTTCCATAGCAGAGCC
ACTCAGAAGAAAAAGTTGGAGTAATACCTCCCAAGAAGTTCATCACAAGATTACGGAAAGAAAATGAGCTTTTTGACAAC
TACATGCGACAGGATCCCCCATGAATTCTTAAATTACCTACTAAATACAATTGCTGATATTTTACAAGAAGAGAGAAAGC
AAGAAAAACAAAATGGCCGCTTACCTAATGGTAATATTAATAATGAAAATAATAACAGCACCCCAGACCCAATGCGGGTT
CATGAGATTTTTCAGGGAACATTAACTAATGAAACCAGATGTCTTACTTGTGAAACTATAAGCAGCAAAGATGAAGATTT
TTTAGACCTGTCTGTTGACGTGGAACAAAATACATCAATTACTCACTGCTTAAGGGCTTTCAGCAACACAGAAACTCTAT
GCAGTGAATACAGGTATTACTGTGAAGAGTATCGCAGCAAACAGGAAGCACACAAACGGAGGAAAGTTTAAAAACTGCCC
ATGATTCTAGCTCCACACCTGAAGAGATTTAAATATAAGGATCAACTTCATCGATTTACAAAACTCTCTTACCAGGTAGT
TTTTCCTTTAAAACTTAGTCTATTTAACACTTCAGGTGATGCCACCAATCCAGACAGAATGTACAGCCTTGTTGCTGTTG
TGGTTCACTGTGGA

Alignment

ORF - retro_ggor_2223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 81.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LCYPGTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQALYFCRPFRENVLAYKAQQKKKENLLT
          .C.....ASALEK.IGPEQFP.NEHYFGLV.FGNTCYCNSVLQALYFCRPFRE.VLA.K.Q..KKE.LLT
Retrocopy ICTMSASASALEKEIGPEQFPVNEHYFGLVSFGNTCYCNSVLQALYFCRPFRETVLA*KSQPRKKESLLT

Parental  CLADLFHSIATQKKK-VGVIPPKKFISRLRKENDLFDNYMQQDA-HEFLNYLLNTIADILQEEKKQEKQN
          CLADLFHS.ATQKKK.VGVIPPKKFI.RLRKEN.LFDNYM.QD..HEFLNYLLNTIADILQEE.KQEKQN
Retrocopy CLADLFHSRATQKKK<VGVIPPKKFITRLRKENELFDNYMRQDP>HEFLNYLLNTIADILQEERKQEKQN

Parental  GKLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSSKDEDFLDLSVDVEQNTSITHCLRDFS
          G.L.NGN.N....N..P....VHEIFQGTLTNETRCL.CET.SSKDEDFLDLSVDVEQNTSITHCLR.FS
Retrocopy GRLPNGNINNENNNSTPDPMRVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRAFS

Parental  NTETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLKRFKYMEQLHRYTKLSYRVVFPLELRLFNTS
          NTETLCSE..YYCE...SKQEA.KR..V.KLPMILA.HLKRFKY..QLHR.TKLSY.VVFPL.L.LFNTS
Retrocopy NTETLCSEYRYYCEEYRSKQEAHKRRKV*KLPMILAPHLKRFKYKDQLHRFTKLSYQVVFPLKLSLFNTS

Parental  SDAVNLDRMYDLVAVVVHCG
          .DA.N.DRMY.LVAVVVHCG
Retrocopy GDATNPDRMYSLVAVVVHCG

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	0.38 RPM	52.17 RPM
SRP007412_cerebellum	0.51 RPM	41.33 RPM
SRP007412_heart	0.13 RPM	10.38 RPM
SRP007412_kidney	0.49 RPM	25.64 RPM
SRP007412_liver	0.16 RPM	6.86 RPM
SRP007412_testis	0.73 RPM	26.31 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_2223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2223 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3266
Pan troglodytes	retro_ptro_2209
Pongo abelii	retro_pabe_2705

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007660	1 retrocopy	retro_cpor_1157,
Gorilla gorilla	ENSGGOG00000017197	3 retrocopies	retro_ggor_1767, retro_ggor_2223 , retro_ggor_2937,