RetrogeneDB ID: retro_ptro_1774

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:33582212..33582821(+)
• Located in intron of: ENSPTRG00000014726

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSPTRG00000014619
• Aliases: SEC13, SEC13L1
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_ptro_1774
GTGGTGTCTGTAATTAACACTGTGGATACCTCCCATAAGGATATGATTCATGATGCCCAGATGGACTACTATGGCACCCG
CCTGGCAACCTGCTCATCAGAAAAATCCGTCAAAATCTTCAAAGTGCACAACAGAGGGCAGATCCTCATTGCCAACCTCA
GAAGTCATGAGAGTCCTATGTGGCAAGTGGCCTGGGCTCACCCCACATATGGCAATATCCTGGCATTGTGCTCCTATGAT
TGGAAAGTCATTATCTGGAAAGAGGAAAACGGCACCTGGGAGAAGACCCACGACCCCTCAGGATATGACTCCTCAGTGAA
CTCTGTATGCTAGGTCCCCCATGACTACGGCCTGATCCTGGCCTGTGGGAGCTCAGATGGGGCCATCTTCCTGCTGACTT
ATACAGGGGAAGGCCAATGGGAAGTGAAGAAGATCAACAACGCTTACACCATTGGCTGCAATGCCGTCAGCTAGGCCCCT
GCTGTTGTACCTGGAAGCCTCATAGACCAGCTGTTCAGGCAGAAACCCAATTACATCAAGAAGTTTCCATCAGGTGGCTG
TGACAACCTCTTCAAGGATGGCCAGTGGAAGGAGAGCAGAAGCTGGAAG

Alignment

ORF - retro_ptro_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 63.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMY
          .VSVINTVDTSH.DMIHDAQMDYYGTRLATCSS..SVKIF.V.N.GQILIA.LR.HE.P.WQVAWAHP.Y
Retrocopy VVSVINTVDTSHKDMIHDAQMDYYGTRLATCSSEKSVKIFKVHNRGQILIANLRSHESPMWQVAWAHPTY

Parental  GNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQW
          GNILA.CSYD.KVIIW.EENGTWEK.H...G.DSSVNSVC..PHDYGLILACGSSDGAI.LLTYTGEGQW
Retrocopy GNILALCSYDWKVIIWKEENGTWEKTHDPSGYDSSVNSVC*VPHDYGLILACGSSDGAIFLLTYTGEGQW

Parental  EVKKISNAHTIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQWK
          EVKKI.NA.TIGCNAVS.APAVVPGSLIDQ...QKPNYIK.F.SGGCDNL.K.....E...WK
Retrocopy EVKKINNAYTIGCNAVS*APAVVPGSLIDQLFRQKPNYIKKFPSGGCDNLFKDGQWKESRSWK

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	0.64 RPM	42.33 RPM
SRP007412_cerebellum	2.01 RPM	28.14 RPM
SRP007412_heart	0.15 RPM	17.84 RPM
SRP007412_kidney	0.31 RPM	72.21 RPM
SRP007412_liver	0.10 RPM	80.43 RPM
SRP007412_testis	0.74 RPM	27.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1774 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1774 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2630
Pongo abelii	retro_pabe_2333

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774 ,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,