RetrogeneDB ID: retro_ggor_1054

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:46325895..46326779(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026783
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSGGOG00000005090
• Aliases: None
• Description: None

Sequence

>retro_ggor_1054
ATGGACGGCATTGTCCCAGATACAGCAGTTGGTACAAAGCGGGGATCTGACGAGCTTTTCTCTGCTTGTGTCACTAACAG
ACCATTTATCATGAGCAGCAACTCGGCCTCTGCAGCAAATGGACATGGCAGCAAGAAGTTCAAAGGTGACAGCAGAAGCG
CCGGTGTCCCCTCCAGAGTGACCCACATTCAGAAGCTCCCATCGACGTCATCGAAAGGGAGGTGATCTCCCTGGAGCTGC
CCTTTGGGAAGGTAACTAACCTCCTGATGCTGAAGGGGAAAAACCAGGCCTTCATCAAGATGAGCACGGAGGAGGCTGCC
AACACCATGGTGAATTACTACACCTCGGTGACGCCCGTGCTGCGCGGCCAGCCCATCTACATCCAGTTCTCCAACCACAA
GGGGCTGAAGACCGACAGCTCTCCCAACCAGGCGCGGGACCCGGCGGCCCTCAGGCTGTGAACTTGGTCCAGTCGGGGAA
CCTGGCCTTGACTGCCCCGGCGGTGGCCGTAGACGCAGGGATGGCGATGGCCGGGCAGAGCCCGGTGCTCAGGATCATCG
TGGAGAACCTCTTCTACCCCATGACCCTGGATGTGCTGCACCAGATTTTCTCCAAGTTCGGCACAGTGAAGACCATCACT
TTCATCAAGGACAACCAGTTCCAGGCCCTGCTGCAGTACACGGACCCCAAGAACGCCCAGCATACCAAGCTGTCGCTGGA
TTGGCAGAACACCTACAACGCCTGCCACACGCTGTGCATCGACTTCTCCAAGCTCATCAGCCTCAACGTAAAGTACAACA
ACGACAAGAGCCGCGACTACCACGCCCAGACCTGCCCTCCGGGGACAGCAAGCCCTCGCTGGACCAGACATGGCCGTGGC
CTTC

Alignment

ORF - retro_ggor_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDGIVPDIAVGTKRGSDELFSTCVTNGPFIMSSNSASAANGNDSKKFKGDSRSAGVPSRVIHIRKLP-ID
          MDGIVPD.AVGTKRGSDELFS.CVTN.PFIMSSNSASAANG..SKKFKGDSRSAGVPSRV.HI.KLP.ID
Retrocopy MDGIVPDTAVGTKRGSDELFSACVTNRPFIMSSNSASAANGHGSKKFKGDSRSAGVPSRVTHIQKLP<ID

Parental  VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD
          V.E.EVISL.LPFGKVTNLLMLKGKNQAFI.M.TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK.LKTD
Retrocopy VIEREVISLELPFGKVTNLLMLKGKNQAFIKMSTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKGLKTD

Parental  SSPNQARAQAAL-QAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG
          SSPNQAR..AAL.QAVN.VQSGNLAL.A.A.AVDAGMAMAGQSPVLRIIVENLFYP.TLDVLHQIFSKFG
Retrocopy SSPNQARDPAAL<QAVNLVQSGNLALTAPAVAVDAGMAMAGQSPVLRIIVENLFYPMTLDVLHQIFSKFG

Parental  TVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY-TR
          TV.K.ITF.K.NQFQALLQY.DP..AQH.KLSLD.QN.YNAC.TL.IDFSKL.SLNVKYNNDKSRDY..R
Retrocopy TV-KTITFIKDNQFQALLQYTDPKNAQHTKLSLDWQNTYNACHTLCIDFSKLISLNVKYNNDKSRDY<PR

Parental  PDLPSGDSQPSLDQT-MAAAF
          PDLPSGDS.PSLDQT.MA.AF
Retrocopy PDLPSGDSKPSLDQT<MAVAF

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	16.02 RPM
SRP007412_cerebellum	0.00 RPM	22.06 RPM
SRP007412_heart	0.00 RPM	18.61 RPM
SRP007412_kidney	0.00 RPM	40.85 RPM
SRP007412_liver	0.05 RPM	36.56 RPM
SRP007412_testis	0.00 RPM	54.60 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_1054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1054 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1354
Pan troglodytes	retro_ptro_928

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054 ,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,