RetrogeneDB ID: retro_ggor_1379

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:43578032..43579032(+)
• Located in intron of: ENSGGOG00000025030

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP18
• Ensembl ID: ENSGGOG00000017061
• Aliases: None
• Description: None

Sequence

>retro_ggor_1379
ATGCCGCGGGAACTGAGGAGCCGAATGAAACTGCACAGTAGAACCGGAGCGAAGCCGAAGCGTTAGCCCGGAACGAGGGC
GGACTGGAAAGCCGGAGCGGGGCTGGGCGGGCCGCCCCAAAAGGCTGCCGCTTCATCCCAGCGAAAACCGCCGGCCAGGC
CAAGCGCGGCGAGGGAAGAGGAGAGAAGGCTCCGGCAGCGGAACCGCCTGACGCTGGAGAAGACAAACCGGCCGTGGAGT
GGTGCCTGGAGGAGCTGGTGGTCTTCGGCGACGTCGACGACGACGAGGACACGCTGCTGCGGCGTCTGCGGGGTCCGCGG
GTTCAAGGACATGAAGACTTGGGAGACTCAGAAGCGGACTATGAGGCAAAAGGTAATTGTGCACCTCAAAAGAAGCCAGT
TTGGGTGGATGAAGAAGATGAAGATGAGGAAATGGTTGACATGATGAACAATCGGTTTCGGAAAGATAATGATGAAAAAT
GCTAGTGAAAGTAAACTTTAGAAAGACAAACTTAAGAAGCGACTTTAAGAAGAATTCCAGCATGCCGTGGGAGGAGTACC
TGCCTGGGCAGAGACTAATAAGCGGAAAACAACTTCAGATGATGAAAGTGAAGAGGATGAAGATGCTTTGTTGCAAAGGA
CTGGGAATTTCATATCCACATCAACTTCTCTTCCAAGAGGAATCCTGAAGATGAAGAACTGCCAGCACGCTAATGCTGAA
CGTCCTTCTGCTGCTCAGATCTCATCTGTGCAGTTCCGTCCTTGTGCACAGATTGTGATGGTCGCTGGATTAGATAACCT
ATATCACTATTTCAGGTTGATGGAAGAACAAATCCTAAAATCCAGAGCACCTGTTTGGAAAGGTTTCCAAACTTTAAGGC
TTGTTTTAGTGCTAATGGGGAAGAAGTTTTAGCCGTGAGTACTCACAGCAAGGTTTTTTATGTCTATGACATGCTAGCTG
GAAATTAATTCCTGTGCATCAAGTGAGAGGTTTGAAAGAA

Alignment

ORF - retro_ggor_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.18 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPPERRRRMKLDRRTGAKPKRKPGMRPDWK--AGAGPGGPPQKPAPSSQPIA--VAAAEEERRLRQRNRL
          MP.E.R.RMKL..RTGAKPKR.PG.R.DWK..AG.G.............P.A...AA.EEERRLRQRNRL
Retrocopy MPRELRSRMKLHSRTGAKPKR*PGTRADWKAGAGLGGPPQKAAASSQRKPPARPSAAREEERRLRQRNRL

Parental  TLE-EDKPAVERCLEELV-FGDVENDEDALLRRLRGPRVQEHEDSGDSEVENEAKGNFPPQKKPVWVDEE
          TLE.EDKPAVE.CLEELV.FGDV..DED.LLRRLRGPRVQ.HED.GDSE...EAKGN..PQKKPVWVDEE
Retrocopy TLE<EDKPAVEWCLEELVVFGDVDDDEDTLLRRLRGPRVQGHEDLGDSEADYEAKGNCAPQKKPVWVDEE

Parental  DEDEEMVDMMNNRFRKD-IMKNASESKLSKDNLKKRLKEEFQHAMGGVPAWAETTKRKTSSDDESEEDED
          DEDEEMVDMMNNRFRKD..MKNASESKL.KD.LKKRL.EEFQHA.GGVPAWAET.KRKT.SDDESEEDED
Retrocopy DEDEEMVDMMNNRFRKD>MMKNASESKL*KDKLKKRL*EEFQHAVGGVPAWAETNKRKTTSDDESEEDED

Parental  DLLQRTGNFISTSTSLPRGILKMKNCQQANAERPTVARISSVQFHPGAQIVMVAGLDN-AVSLFQVDGKT
          .LLQRTGNFISTSTSLPRGILKMKNCQ.ANAERP..A.ISSVQF.P.AQIVMVAGLDN...SLFQVDG.T
Retrocopy ALLQRTGNFISTSTSLPRGILKMKNCQHANAERPSAAQISSVQFRPCAQIVMVAGLDN<PISLFQVDGRT

Parental  NPKIQSIYLERFPIFKACFSANGEEVLATSTHSKVLYVYDMLAG-KLIPVHQVRGLKE
          NPKIQS..LERFP.FKACFSANGEEVLA.STHSKV.YVYDMLAG.KLIPVHQVRGLKE
Retrocopy NPKIQSTCLERFPNFKACFSANGEEVLAVSTHSKVFYVYDMLAG<KLIPVHQVRGLKE

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	11.13 RPM
SRP007412_cerebellum	0.00 RPM	12.88 RPM
SRP007412_heart	0.03 RPM	1.81 RPM
SRP007412_kidney	0.04 RPM	15.82 RPM
SRP007412_liver	0.11 RPM	8.89 RPM
SRP007412_testis	4.66 RPM	55.74 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_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1379 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1882

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001477	1 retrocopy	retro_cpor_657,
Homo sapiens	ENSG00000011260	1 retrocopy	retro_hsap_1882,
Gorilla gorilla	ENSGGOG00000017061	1 retrocopy	retro_ggor_1379 ,
Myotis lucifugus	ENSMLUG00000016938	1 retrocopy	retro_mluc_2308,
Mustela putorius furo	ENSMPUG00000015582	1 retrocopy	retro_mputfur_646,
Vicugna pacos	ENSVPAG00000010164	1 retrocopy	retro_vpac_170,