RetrogeneDB ID: retro_ptro_357

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:152847967..152848551(-)
• Located in intron of: ENSPTRG00000001703

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSPTRG00000015796
• Aliases: None
• Description: None

Sequence

>retro_ptro_357
CCACGTCTAAGTGACAAGAATACAGAACACTATTTTCCAGTGTTAAAAAGAAAGGCAAGCCTTCTGAAGCAAAATGAAGT
GCATAGGAAACCAGTTGCAGTTCTCAAGAGACCTAACCAGCTAAACAGAAAAAATAACATTATGGCCAGTTTTACCAGGA
GAGGAAATAAATTAAGCCATCAGAAAGACACTTCACAGGTAACTTTTCTTTTCGGAAGAGGCCTGAAGAAGGTTCAGGCC
CAGTTGAACACGGAACAACTGCTAGATGTAGTAGCAAAGAGAACTAGTCAATGCCAGACTTCTATCACAAACGCAGGAAT
CTGACTGTATCTATTGATAACCCTGGAGCAGTACAATGCCCAGCAACTGAGAAACCATGATTAATTCATACTGCTATACC
TTCATTCTTTAAAACACGGCAGCAAGAGAATGTAAAGAAAGTTCCAACGGGTGTTCCCCTACAATTTGACATAAATAGTG
TTGGAAAACAGACAGAGATGGCTTTGAATGAGCACTTTGGGATCCTGAGAAAACAAAGAGCCACTCTCACATATAACAAA
GGAGGAAGTCATTTTTTAACTGTG

Alignment

ORF - retro_ptro_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.66 %
• Parental protein coverage: 61.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPLSDKNIEQYFPVLKRKANLLRQNEGQRKPVAVLKRPSQLSRKNNIPANFTRSGNKLNHQKDTRQATFL
          P.LSDKN.E.YFPVLKRKA.LL.QNE..RKPVAVLKRP.QL.RKNNI.A.FTR.GNKL.HQKDT.Q.TFL
Retrocopy PRLSDKNTEHYFPVLKRKASLLKQNEVHRKPVAVLKRPNQLNRKNNIMASFTRRGNKLSHQKDTSQVTFL

Parental  FRRGL-KVQAQLNTEQLLDDVVAKRTRQWRTSTTNGGI-LTVSIDNPGAVQCPVTQKPRLTRTAVPSFLT
          F.RGL.KVQAQLNTEQLL.DVVAKRT.Q..TS.TN.GI.LTVSIDNPGAVQCP.T.KP.L..TA.PSF..
Retrocopy FGRGLKKVQAQLNTEQLL-DVVAKRTSQCQTSITNAGI<LTVSIDNPGAVQCPATEKP*LIHTAIPSFFK

Parental  KREQSDVKKVPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTYNKGGSRFVTV
          .R.Q..VKKVP.GVPLQFDINSVGKQT.M.LNE.FGIL..QRATLTYNKGGS.F.TV
Retrocopy TRQQENVKKVPTGVPLQFDINSVGKQTEMALNEHFGILRKQRATLTYNKGGSHFLTV

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	29.39 RPM
SRP007412_cerebellum	0.00 RPM	43.52 RPM
SRP007412_heart	0.00 RPM	71.32 RPM
SRP007412_kidney	0.03 RPM	49.14 RPM
SRP007412_liver	0.00 RPM	28.02 RPM
SRP007412_testis	0.00 RPM	92.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_357 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_357 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_476
Gorilla gorilla	retro_ggor_450
Pongo abelii	retro_pabe_258
Macaca mulatta	retro_mmul_577
Callithrix jacchus	retro_cjac_1639

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357 ,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,