RetrogeneDB ID: retro_ptro_2032

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:167050195..167050799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ptro_2032
CTTTCCGTGGCCTACATGAGTGTGGTTGCGGGCTGCAGGTCCACCTGCAGGGTCATCTTAAACATCGAGCAGAAGACAGA
CACCTCCGACAAGAAGTTGCAGCTGATTAAGGACTACCAGGAGAAAGTGGAGTCTGAGCTGAGATCGATCTGCACCACGG
TCCTGGAATTGTTGGATAAATATTTAACAGCCAATGCAACTAATCCAGAGAGTGGGGTCTTCTATCTGAAAATGAAGGGT
GATTACTTCCAGTACTTTGCTGAAGTTGCATGTGGTAATGATCAAAAACAAATGATAGATAATTCCCAAGGAGCTTACCA
AAAGGCATTTGATATAAGCAAGAAAGAGATACAATCCACACATCCAATCTGCCTGGGGCTTGCTGTTAACTTTTCTGTAT
TTTACTATGAGATTCTTAATAACCCAGAGCTTGCCTGCATGCTGGCTAAAACGGCTTTTGATGAGGCCATTGCAGAACTT
GATACACTGAATGAAGATTCATCCAAAAGACAGCACCCTCATTATGGAGTTTCTTAGAGACAACCTAACACTATGGACCT
CAGACAGTGCAGGAGCAGAATGTGATGCAGCAGAAGGGGCTGAA

Alignment

ORF - retro_ptro_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.63 %
• Parental protein coverage: 82.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVAYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPE
          LSVAY..VV.G.RS..RVI..IEQKTDTSDKKLQLIKDY.EKVESELRSICTTVLELLDKYL.ANATNPE
Retrocopy LSVAYMSVVAGCRSTCRVILNIEQKTDTSDKKLQLIKDYQEKVESELRSICTTVLELLDKYLTANATNPE

Parental  SKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILN
          S.VFYLKMKGDYF.Y.AEVACG.D.KQ.IDNSQGAYQ.AFDISKKE.Q.THPI.LGLA.NFSVFYYEILN
Retrocopy SGVFYLKMKGDYFQYFAEVACGNDQKQMIDNSQGAYQKAFDISKKEIQSTHPICLGLAVNFSVFYYEILN

Parental  NPELACTLAKTAFDEAIAELDTLNEDSY-KDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAE
          NPELAC.LAKTAFDEAIAELDTLNEDS..KDSTLIM..LRDNLTLWTSDSAG.ECDAAEGAE
Retrocopy NPELACMLAKTAFDEAIAELDTLNEDSS>KDSTLIMEFLRDNLTLWTSDSAGAECDAAEGAE

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	181.50 RPM
SRP007412_cerebellum	0.00 RPM	164.19 RPM
SRP007412_heart	0.00 RPM	61.38 RPM
SRP007412_kidney	0.03 RPM	105.78 RPM
SRP007412_liver	0.00 RPM	49.92 RPM
SRP007412_testis	0.11 RPM	224.57 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2032 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2032 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3004
Gorilla gorilla	retro_ggor_2081
Pongo abelii	retro_pabe_2490

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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,