RetrogeneDB ID: retro_ptro_1655

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:156592595..156593353(+)
• Located in intron of: ENSPTRG00000012541

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSPTRG00000000395
• Aliases: None
• Description: None

Sequence

>retro_ptro_1655
CAGAAGGCCCGGTGGGAGAAGAGAGCCCGGGGGAAGGTGGAGAGGGTGGCCAGGCTGGCCAAGGAAGCCAAGTCAGAGAC
CTCGGGGCCCCAGATAAAGGCAGACAGACAGAGAGGCTGCAGCTAGAGATTGACCAGAAAAAGGATGCAGAGAATCATGA
GGCCCAGCTCAAGAACGGCAGCCTTGACTCCCCAGGAAAGCAGGAGAAGAAGGAGGAAGATGAGAAGGACAAAGGAAAAC
TGAAGCCCAACCTAGGCAACGGGGCAGACCTGCCCAATTACCGCTGGACCCAGAGCCTGTCGGAGCTGGACCTGGTGGTC
CCTTTCTGTGTAAACTTCCGGCTGAAAGGGAAGGACATGGTGGTGGACATCCAGGTGCAGCACCTCTGGGTGGGGCTCAA
GGGGCAGCCAGCGATCATCGATGGGGAGCTCTACAACGAAGTGAAGGTAGGGGAGAGCTTGTGGCTCATTGAGGACGGCA
AGGTGGTGACTGTGCATCTTGAGAAGATCAATAAGATGGAGTGGTGGAGCTGCTTGGTGTCCAGTGACCCTGAGATCAAT
ACCAAGATGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAATGAGACTCGCAGCATGGTGGAAAAGATGATGTA
TGACCAGAGACAGAAGTCCATGGGGCTGCCAATCTCAGACGAACAGAAGAAACAGGAGATTCTGAAGAAGTTCATGGATC
AGCATCTGGAGATGGATTTTTCCAAGGCCAAATTCAAC

Alignment

ORF - retro_ptro_1655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 78.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRARQEAERREKAERAARLAKEAKSETSGPQIKELTDE-EAERLQLEIDQKKDAENHEAQLKNGSLDSPG
          ..AR.E...R.K.E...R.A..AK...S.............ERLQLEIDQKKDAENHEAQLKNGSLDSPG
Retrocopy QKARWEKRARGKVE---RVARLAKEAKSETSGPQIKAD<QTERLQLEIDQKKDAENHEAQLKNGSLDSPG

Parental  KQETEEDEEEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFCVNFRLKGKDVVVDIQRRHLRVG
          K........EEDEKDKGKLKPNLGNGADLPNYRWTQ.LSELDL.VPFCVNFRLKGKD.VVDIQ..HL.VG
Retrocopy K----QEKKEEDEKDKGKLKPNLGNGADLPNYRWTQSLSELDLVVPFCVNFRLKGKDMVVDIQVQHLWVG

Parental  LKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEINTKKINPENSKLSDLD
          LKGQPAIIDGELYNEVKV.ES.WLIEDGKVVTVHLEKINKMEWWS.LVSSDPEINTK.INPENSKLSDLD
Retrocopy LKGQPAIIDGELYNEVKVGESLWLIEDGKVVTVHLEKINKMEWWSCLVSSDPEINTKMINPENSKLSDLD

Parental  SETRSMVEKMMYDQRQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          .ETRSMVEKMMYDQRQKSMGLP.SDEQKKQEILKKFMDQH.EMDFSKAKFN
Retrocopy NETRSMVEKMMYDQRQKSMGLPISDEQKKQEILKKFMDQHLEMDFSKAKFN

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	0.89 RPM	159.28 RPM
SRP007412_cerebellum	0.65 RPM	149.92 RPM
SRP007412_heart	0.15 RPM	61.24 RPM
SRP007412_kidney	0.29 RPM	98.30 RPM
SRP007412_liver	0.16 RPM	149.37 RPM
SRP007412_testis	0.32 RPM	133.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1655 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1655 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2168
Gorilla gorilla	retro_ggor_1720
Pongo abelii	retro_pabe_2055

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655 , retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,