RetrogeneDB ID: retro_ptro_3120

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:69778600..69779114(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000028260
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSPTRG00000020413
• Aliases: None
• Description: OTU domain containing 6B [Source:HGNC Symbol;Acc:24281]

Sequence

>retro_ptro_3120
GAGGGAGAGCCACGAGAGCATCTTTTCCAGGCTGAGATGTCGGAGCACCTGGCCCGGCTTCCAGCGCGAGGAGGAGGAGA
AGCTCGCCGCCATCCTGGGAGCCAGGGGTCTGGAGATGAAAGCGATCCCGGCCGACGGCCACTGCATGTACCGCGCCATC
CAAGACCAGCTGGTGTTCAGCGAATCTGTGGAGATGGTGCGCTGCCGCACCGCCAGCTACATGAAGGAGCACGTGGACGA
CTTCCTGCCCTTTTTCAGCAACCCCGAGACCAGCGACTCCTTCGGGTACGACGACTTCATGATCTACTGCGACAACATCG
TGCGCACCGCGGCATGGGGAGGCCAGCTGGAGCTGAGGGCCCTGTCGCACGTCCTGAAGACCCCCATCGAGGTGATCCAG
GCCGACTCGCCCAACTTGGTCATCGGGGAGGAGTACGTCAAGAAGCCGATCATCCTGGTCTACCTGCGCTATGCCTACAG
CCTCGGCGAGCACTACAACTCCGTGACACCGCTC

Alignment

ORF - retro_ptro_3120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.57 %
• Parental protein coverage: 53.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKEREERIAEAEI-ENLT-GARHMESEKLAQILAARQLEIKQIPSDGHCMYRAIEDQLKEKDCALTVVAL
          E.E..E....AE..E.L..G....E.EKLA.IL.AR.LE.K.IP.DGHCMYRAI.DQL........V...
Retrocopy EGEPREHLFQAEMSEHLA>GFQREEEEKLAAILGARGLEMKAIPADGHCMYRAIQDQLVFSE---SVEMV

Parental  RSQTAEYMQSHVEDFLPFLTNPNTGDMYTPEEFQKYCEDIVNTAAWGGQLELRALSHILQTPIEIIQADS
          R..TA.YM..HV.DFLPF..NP.T.D......F..YC..IV.TAAWGGQLELRALSH.L.TPIE.IQADS
Retrocopy RCRTASYMKEHVDDFLPFFSNPETSDSFGYDDFMIYCDNIVRTAAWGGQLELRALSHVLKTPIEVIQADS

Parental  PPIIVGEEYSKKPLILVYMRHAYGLGEHYNSVTRL
          P....GEEY.KKP.ILVY.R.AY.LGEHYNSVT.L
Retrocopy PNLVIGEEYVKKPIILVYLRYAYSLGEHYNSVTPL

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	6.11 RPM
SRP007412_cerebellum	0.00 RPM	8.96 RPM
SRP007412_heart	0.03 RPM	6.91 RPM
SRP007412_kidney	0.00 RPM	7.82 RPM
SRP007412_liver	0.00 RPM	3.37 RPM
SRP007412_testis	0.63 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3120 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120 ,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,