RetrogeneDB ID: retro_ptro_2405

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:156274266..156275001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf203
• Ensembl ID: ENSPTRG00000018464
• Aliases: None
• Description: chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]

Sequence

>retro_ptro_2405
GTTATAAGTGCCATGGCTATGACTAGTGTCAAATTGCATGCTGGTGTTTTAAGAAAGCCAGATACCTGGATTGGACTCTG
GGGTGTTCTCTGAGGAACACCTTCATCACACAAACTCTGTACTTCCTGGAATCAGTACTTGTATTTTTCTAGTACCAAGT
TACATGCACCAAATTATAAAACACTTTTCCATAACATTTTCTCACTGAGACTCCCGGGGCTTTTAATATCTCTGGAATAT
TTTTTTCCATTTTCCATAAGACTCAAAAGTAATATAAGCTCTACAAAATCTAGTAAAAAGTATCGGCAAAAAACAGGAGA
TGAGGAGGACTCTGATGCAGAAAGTGATCAGAACGAGATGAGTGAGCAGGAAGAGGAGCTTGAGGATGGCCTTACTATAG
CAAAGACTATCAAGACCTGGAAACAGTAGTGCGGTCTTTTCAGGATGACGTTGTCCTGAAGACAAGCCTGGATATTGGAA
GAAACAAAGTGGGAGATGCATTCTGCAAAGGTGAATTCAGGCTGAATGGGGAAAAATTATGGAAGAAAAGCAGAATGGTC
AAAGTGGGAGATACATTGGATCTTCTCATTGGAGAGGATAAGGAAGCAGGAACAGAGACAGTGATGCAGATTCTCCCAAA
AAAAAGTGTTTGAAGAGAAGACTGAAAGTGACAAATACACAGTGGTATTACAGCAGTGGGAAAACTTAAAAATGCCTAAG
AAGAGAATGTCTAAA

Alignment

ORF - retro_ptro_2405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.54 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IISAMAMASVKLLAGVLRKPDAWIGLWGVLRGTPSSYKLCTSWNRYLYFSSTKLRAPNYKTLFYNIFSLR
          .ISAMAM.SVKL.AGVLRKPD.WIGLWGVL.GTPSS.KLCTSWN.YLYFSSTKL.APNYKTLF.NIFSLR
Retrocopy VISAMAMTSVKLHAGVLRKPDTWIGLWGVL*GTPSSHKLCTSWNQYLYFSSTKLHAPNYKTLFHNIFSLR

Parental  LPGLLLSPECIFPFSVRLKSNIRSTKSTKKSLQKV-DEEDSDEESDHDEMSEQEEELEDDPTVV-KNYKD
          LPGLL.S.E..FPFS.RLKSNI.STKS.KK..QK..DEEDSD.ESD..EMSEQEEELED..T...K.Y.D
Retrocopy LPGLLISLEYFFPFSIRLKSNISSTKSSKKYRQKTGDEEDSDAESDQNEMSEQEEELEDGLTIA<KDYQD

Parental  LEKAVQSFRYDVVLKTGLDIGRNKVEDAFYKGELRLNEEKLWKKSRTVKVGDTLDLLIGEDKEAGTETVM
          LE..V.SF..DVVLKT.LDIGRNKV.DAF.KGE.RLN.EKLWKKSR.VKVGDTLDLLIGEDKEAGTETVM
Retrocopy LETVVRSFQDDVVLKTSLDIGRNKVGDAFCKGEFRLNGEKLWKKSRMVKVGDTLDLLIGEDKEAGTETVM

Parental  RIL-LKKVFEEKTESEKYRVVLRRWKSLKLPKKRMSK
          .IL....VFEEKTES.KY.VVL..W..LK.PKKRMSK
Retrocopy QIL>XXXVFEEKTESDKYTVVLQQWENLKMPKKRMSK

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	6.43 RPM
SRP007412_cerebellum	0.00 RPM	6.52 RPM
SRP007412_heart	0.03 RPM	10.26 RPM
SRP007412_kidney	0.00 RPM	10.85 RPM
SRP007412_liver	0.00 RPM	6.45 RPM
SRP007412_testis	0.00 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2405 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2405 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3538
Gorilla gorilla	retro_ggor_2389

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003732	1 retrocopy	retro_cfam_1818,
Homo sapiens	ENSG00000130349	1 retrocopy	retro_hsap_3538,
Gorilla gorilla	ENSGGOG00000006113	1 retrocopy	retro_ggor_2389,
Macropus eugenii	ENSMEUG00000013534	1 retrocopy	retro_meug_2181,
Microcebus murinus	ENSMICG00000004137	1 retrocopy	retro_mmur_1269,
Macaca mulatta	ENSMMUG00000007391	1 retrocopy	retro_mmul_115,
Nomascus leucogenys	ENSNLEG00000013450	2 retrocopies	retro_nleu_1433, retro_nleu_499,
Otolemur garnettii	ENSOGAG00000008839	2 retrocopies	retro_ogar_1396, retro_ogar_390,
Pongo abelii	ENSPPYG00000016885	1 retrocopy	retro_pabe_2922,
Pan troglodytes	ENSPTRG00000018464	2 retrocopies	retro_ptro_1453, retro_ptro_2405 ,
Tursiops truncatus	ENSTTRG00000008837	2 retrocopies	retro_ttru_324, retro_ttru_432,