RetrogeneDB ID: retro_ptro_928

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:64369821..64370705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSPTRG00000010165
• Aliases: None
• Description: None

Sequence

>retro_ptro_928
ATGGACGGCATTGTCCCAGATATAGCAGTTGGTACAAAGCGGGGATCTGACGAGCTTTTCTCTGCTTGTGTCACTAACAG
ACCATTTATCATGAGCAGCAACTCGGCCTCTGCAGCAAATGGACATGGCAGCAAGAAGTTCAAAGGTGACAGCAGAAGCG
CCCGTGTCCCCTCCAGAGTGACCCACATCCAGAAGCTCCCATCGACGTCATCGAAGGGGAGGTGATCTCCCTGGAGCTGC
CCTTTGGGAAGGTCATTAACCTCCTGATGCTGAAGGGGAAAAACCAGGCCTTCATCAAGATGAGCACGGAGGAGGCTGCC
AACACCATGGTGAATTACTACACCTCGGTGACGCCCGTGCTGCGCGGCCAGCCCATCTACATCCAGTTCTCCAACCACAA
GGGGCTGAAGACCGACAGCTCTCCCAACCAGGCGCGGGACCCGGCGGCCCTCAGGCCGTGAACTCGGTCCAGTCGGGGAA
CCTGGCCTGGACTGCCCCGGAGGCGGCCGTAGACGCAGGGATGGGGATGGCCGGGCAGAGCCCGGTGCTCAGGATCATCG
TGGAGAACCTCTTCTACCCCATGACCCTGGATGTGCTGCACCAGATTTTCTCCAAGTTCGGCACAGTGAAGACCATCACA
TTCATCAAGGACAACCAGTTCCAGGCCCTGCTGCAGTACACGGACCCCGAGAACGCCCAGCATACCAAGCTGTCGCTGGA
TTGGCAGAACACCTACAACGCCTGCCACACGCTGTGCATCGACTTCTCCAAGCTCATCAGCCTCAACGTAAAGTACAGCA
ACGACAAGAGCCGCGACTACCACGCCCAGACCTGCCCTCCGGGGACAGCTAGCCCTCGCTGGACCAGACATGGCCGTGGC
CTTC

Alignment

ORF - retro_ptro_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.05 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDGIVPDIAVGTKRGSDELFSTCVTNGPFIMSSNSASAANGNDSKKFKGDSRSAGVPSRVIHIRKLP-ID
          MDGIVPDIAVGTKRGSDELFS.CVTN.PFIMSSNSASAANG..SKKFKGDSRSA.VPSRV.HI.KLP.ID
Retrocopy MDGIVPDIAVGTKRGSDELFSACVTNRPFIMSSNSASAANGHGSKKFKGDSRSARVPSRVTHIQKLP<ID

Parental  VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD
          V.EGEVISL.LPFGKV.NLLMLKGKNQAFI.M.TEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK.LKTD
Retrocopy VIEGEVISLELPFGKVINLLMLKGKNQAFIKMSTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKGLKTD

Parental  SSPNQARAQAAL-QAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG
          SSPNQAR..AAL.QAVNSVQSGNLA..A..AAVDAGM.MAGQSPVLRIIVENLFYP.TLDVLHQIFSKFG
Retrocopy SSPNQARDPAAL<QAVNSVQSGNLAWTAPEAAVDAGMGMAGQSPVLRIIVENLFYPMTLDVLHQIFSKFG

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

Parental  PDLPSGDSQPSLDQT-MAAAF
          PDLPSGDS.PSLDQT.MA.AF
Retrocopy PDLPSGDS*PSLDQT<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	0.02 RPM	23.34 RPM
SRP007412_cerebellum	0.04 RPM	39.29 RPM
SRP007412_heart	0.00 RPM	27.48 RPM
SRP007412_kidney	0.03 RPM	168.44 RPM
SRP007412_liver	0.03 RPM	168.68 RPM
SRP007412_testis	0.00 RPM	33.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_928 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_928 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1354
Gorilla gorilla	retro_ggor_1054

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 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 ,
Pan troglodytes	ENSPTRG00000010941	1 retrocopy	retro_ptro_1043,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,