RetrogeneDB ID: retro_ptro_258

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:212059218..212059790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSPTRG00000021465
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_ptro_258
CAGGAAGATGAGCAAGACTGAGAGGAGATTTGATTCAAGCTGAAAGAGACCGGGGAGGTGCAGGACTTGAGGAAGAAACT
AGACATGTGAGAGCTGTGGCCCTGCAGATGGGAGAGGGGATACAAGTGGAGGCCACTCTAGTGGGTGATTTCCTTCAGAT
TAAGACAGGTAGTATGTATATGGGGCAGGAGGAGAAGGGCATGGATGGGATCAGTAAAGAGGAAGACCTCCAGCCAAGGA
TGTCATTTTCTGAAGAAACTAATCCAGGGTAGGAAGGCATGAGCGTGATGAAGTACATGGAGACAAAGACAAAGCAAAGG
AAAGGGCTCCTGGACCACAGGAACAGAAAATCAAACTGAAGAGTGCAGAGGACTGTCTCTATGAACTTTCAGAAAACACA
TGTTTGCTCCTCAAAGAAGGCCAAGGAGATGCTTCCCACCCAATGCTGGGTGCATCCCAAGGTGGATGTCTGCACTGATG
CTGAAATAGAATGCATTGCCACCAAGGAAGCTAAAGCCTGGCTGCTAGCAGAGGATCAGAATAAGAAGAAAGACATTGAG
ACATCTTGTGTG

Alignment

ORF - retro_ptro_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.27 %
• Parental protein coverage: 67.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEDEQDSEEVRLKLEETREVQNLRKR-PNGVSAVALLVGEKVQEETTLVDDPFQMKTGGMVDMKKLKERG
          .EDEQD.EE...KL.ET.EVQ.LRK.....V.AVAL..GE..Q.E.TLV.D..Q.KT.G...M....E.G
Retrocopy QEDEQD*EEI*FKLKETGEVQDLRKK<TRHVRAVALQMGEGIQVEATLVGDFLQIKT-GSMYMGQ-EEKG

Parental  KDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEH-EEQKVKPKNAEDCLYELPENIRV
          .D.IS.EEDL....SFS.ETN...E....MKY.ET..K.RKG...H..EQK.K.K.AEDCLYEL.EN...
Retrocopy MDGISKEEDLQPRMSFSEETNPG*EGMSVMKYMETKTKQRKGLLDH<QEQKIKLKSAEDCLYELSENTCL

Parental  -SSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQNKKKDSETSFV
          .SS.K...EML..Q.....P.VD...DA.I...I.T..AKA.LLAE.QNKKKD.ETS.V
Retrocopy >SSKK-AKEMLPTQCWVH-PKVDVCTDAEIE-CIATKEAKAWLLAEDQNKKKDIETSCV

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	39.65 RPM
SRP007412_cerebellum	0.00 RPM	76.32 RPM
SRP007412_heart	0.09 RPM	39.43 RPM
SRP007412_kidney	0.00 RPM	46.29 RPM
SRP007412_liver	0.00 RPM	37.58 RPM
SRP007412_testis	0.63 RPM	106.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_258 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_258 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_320
Callithrix jacchus	retro_cjac_1757
Bos taurus	retro_btau_1138
Equus caballus	retro_ecab_174

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258 ,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,