RetrogeneDB ID: retro_ptro_3

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:26865082..26865829(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000030723
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSPTRG00000011641
• Aliases: None
• Description: None

Sequence

>retro_ptro_3
ATGGAGAGAGCCAGTCTGATCCAGAAGGCCAAGCTGGCAGAGCAGGCCGAACGCTATGAGGACATGGCAGCCTTCATGAA
AGGCGCCGTGGAGAAGGGCGAGGAGCTCTCCTGCGAAGAGCGAAACCTGCTCTCAGTAGCCTATAAGAACGTGGTGGGCG
GCCAGAGGGCTGCCTGGAGGGTCCTGTCCAGTATTGAGCAGAAAAGCAACGAGGAGGGCTCGGAGGAGAAGGGCCCCGAG
GTGCGTGAGTACCGGGAGAAGGTGGAGACTGAGCTCCAGGGCGTGTGCGACACCGTGCTGGGCCTGCTGGACAGCCACCT
CATCAAGGAGGCCGGGGACGCCGAGAGCCGGGTCTTCTACCTGAAGATGAAGGGTGACTACTACCGCTACCTGGCCGAGG
TGGCCACCGGTGACGACAAGAAGCGCATCATTGACTCAGCCCGGTCAGCCTACCAGGAGGCCATGGACATCAGCAAGAAG
GAGATGCCGCCCACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCCGTCTTCCACTACGAGATCGCCAACAGCCC
CGAGGAGGCCATCTCTCTGGCCAAGACCACTTTCGACGAGGCCATGGCTGATCTGCACACCCTCAGCGAGGACTCCTACA
AAGACAGCACCCTCATCATGCAGCTGCTGCGAGACAACCTGACACTGTGGACGGCCGACAACGCCGGGGAAGAGGGGGGC
GAGGCTCCCCAGGAGCCCCAGAGCTGA

Alignment

ORF - retro_ptro_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.85 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          ME...LIQKAKLAEQAERY.DMA..MK...E.G.ELS.EERNLLSVAYKNVVGG.R.AWRV.SSIEQK..
Retrocopy MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSN

Parental  T--SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDR
          ...S..K......YREKVE.EL...C.TVL.LLD..LI..A...ES.VFYLKMKGDY.RYLAEVA.GDD.
Retrocopy EEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDK

Parental  KQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNE
          K..ID....AYQEA.DISKKEM.PT.PIRLGLALNFSVF.YEI.N.PE.A..LAKT.FDEA.A.L.TL.E
Retrocopy KRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSE

Parental  DSYKDSTLIMQLLRDNLTLWTSDSAGEE
          DSYKDSTLIMQLLRDNLTLWT.D.AGEE
Retrocopy DSYKDSTLIMQLLRDNLTLWTADNAGEE

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	0.05 RPM	181.50 RPM
SRP007412_cerebellum	0.11 RPM	164.19 RPM
SRP007412_heart	0.03 RPM	61.38 RPM
SRP007412_kidney	0.39 RPM	105.78 RPM
SRP007412_liver	0.92 RPM	49.92 RPM
SRP007412_testis	0.21 RPM	224.57 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_8
Gorilla gorilla	retro_ggor_211
Pongo abelii	retro_pabe_103
Callithrix jacchus	retro_cjac_31
Mus musculus	retro_mmus_163
Oryctolagus cuniculus	retro_ocun_248
Bos taurus	retro_btau_86
Sus scrofa	retro_sscr_35
Canis familiaris	retro_cfam_233
Equus caballus	retro_ecab_31

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3 ,
Pan troglodytes	ENSPTRG00000013529	12 retrocopies	retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,