RetrogeneDB ID: retro_ptro_1760

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:18803747..18804899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSPTRG00000021229
• Aliases: None
• Description: Pan troglodytes RAD23 homolog B (S. cerevisiae) (RAD23B), mRNA. [Source:RefSeq mRNA;Acc:NM_001244709]

Sequence

>retro_ptro_1760
GTGAAAGCACTGAAAGAGAAGACGGAATCTGAAAAGGGGAAAGATGCCTCTCTGGTAGCAGGTCAAATATTAATTTATGC
AGGCAAAATCCTCAATGATGATACTGCTCTCAAAGAATATAAAATTGATGAGAAAAACTCTGTGGTGGTTATGGTGACCA
AACCCAAAGCAGTGTCCACACCAGCACTAGCTGCAACTCAGCAGTCAGCTCCTGCCAGCACTACAGCAGTTACTTCCTCC
ACAACAACAACTGTGGCTCAGGCTCCAACCCCTGTCCCTGCTTTGGCTCCCACTTTCACACCTGCATTCATCCCTCCAGT
ATCAGTGACAGTGTCCTCTGAACCTGCAACTGCTAGTGCAACTAAACAAGAGAAACCTGCAGAAAAGCCAGCAGAGACAC
CAGTGGCTACTAGCCTGACATCAACTCATAGTACATCAGGAGATTCTTCTTGGTCAAACCTTTTTGAAGATGCAACGATT
GCACTTGTGATGGGTCAGTCTTACGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGAGAGCAAGTAATTGC
AGCCCCAAGAGCCAGTTCCAACAACCCTGACAGGGCAGTGGAGTACCTTTTAATGGGAATCCCTGGAGATAAAGTCAGGT
TGTGGTTGACCCCCACCAAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAACAGTGGCTGCAGCTGCAGCAACTACGACAG
CAACAACTACAGCAAGTTCTGGAACGTCCCCTTGAATTTTTATGGAATCAGCCTCAGTTTCAACAGATGAGACAAATTAT
TCAACAGAGTCCTTCCCTTCTTCCAGTGTTACTACAGTAGATAGATTGAGAGAATCCTCAATTACTTCAGCAAATTAGCC
AACACCAGGAGCATTTTATTCAGATGTTAAATGAAACAGTTTGAGAAGCTGGTGGTCAAAGAGGAAGAGGTGGAGGTGTC
AGTGGAGGAATTGCAGAAGCTGGAAATGGTCTTATGAACTACATTCAAGTAATGCCTCAGGAAAAAGAAGCTATAGAAAG
GTTAAAGGCATTAGGATTTCCTGAAGGACTTGTGATACAAGCATATTTTGCTTGTGAGAAGAATAAGAATTTGGGTGCCG
ATTTTCTTCTACAGCAGAACTTTGATGAAGAT

Alignment

ORF - retro_ptro_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVSTPAPATTQQSA
          VKALKEK.ESEKGKDA..VAGQ.LIYAGKILNDDTALKEYKIDEKN.VVVMVTKPKAVSTPA.A.TQQSA
Retrocopy VKALKEKTESEKGKDASLVAGQILIYAGKILNDDTALKEYKIDEKNSVVVMVTKPKAVSTPALAATQQSA

Parental  PASTTAVTCSTTTTVAQAPIPVPALAPTSTPASITPASATASSEPAPASAAKQEKPAEKPAETPVATSPT
          PASTTAVT.STTTTVAQAP.PVPALAPT.TPA.I.P.S.T.SSEPA.ASA.KQEKPAEKPAETPVATS.T
Retrocopy PASTTAVTSSTTTTVAQAPTPVPALAPTFTPAFIPPVSVTVSSEPATASATKQEKPAEKPAETPVATSLT

Parental  ATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLM-GIPG
          .T.STSGDSS.SNLFEDAT.ALV.GQSYENMVTEIMSMGYEREQVIAA.RAS.NNPDRAVEYLLM.G.P.
Retrocopy STHSTSGDSSWSNLFEDATIALVMGQSYENMVTEIMSMGYEREQVIAAPRASSNNPDRAVEYLLM<GNPW

Parental  DRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGGHP-LEF-LRNQPQFQQMRQIIQQNPSLL
          .R.SQ.VVDP.QAASTGAPQSS.VAAAAATTTATTT..SSG..P.L.F.L.NQPQFQQMRQIIQQ.PSLL
Retrocopy -R*SQVVVDPHQAASTGAPQSSTVAAAAATTTATTT-ASSGTSP<LNF<LWNQPQFQQMRQIIQQSPSLL

Parental  PALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEA
          P.LLQ.I..ENPQLLQQISQHQEHFIQMLNE.V.EAGGQ.G.GGG.SGGIAEAG.G.MNYIQV.PQEKEA
Retrocopy PVLLQ*ID*ENPQLLQQISQHQEHFIQMLNETV*EAGGQRGRGGGVSGGIAEAGNGLMNYIQVMPQEKEA

Parental  IERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          IERLKALGFPEGLVIQAYFACEKN.NL.A.FLLQQNFDED
Retrocopy IERLKALGFPEGLVIQAYFACEKNKNLGADFLLQQNFDED

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	0.21 RPM	44.45 RPM
SRP007412_cerebellum	0.14 RPM	64.78 RPM
SRP007412_heart	0.35 RPM	55.41 RPM
SRP007412_kidney	0.44 RPM	52.46 RPM
SRP007412_liver	0.20 RPM	73.55 RPM
SRP007412_testis	0.53 RPM	147.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1760 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1760 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1829

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760 ,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,