RetrogeneDB ID: retro_ptro_2813

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:20640132..20640653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMN1
• Ensembl ID: ENSPTRG00000016955
• Aliases: SMN1, SMN2
• Description: None

Sequence

>retro_ptro_2813
ATGGCAATGGGCAGTGCCAGCAGTGTTTGTGGCATCCTGGAGCAGGAAGATTTGGTGCATTTCTAGTGCAGCATAGGCCA
GAGTGACGTTTCTGACATTTGGGATGCTACAGCACTGATAGAAGTGGATGATAAAGCTGTGGCTTCTTTTAAACAGGCTC
TAAAGAATGATGACATTTGTGAAACCTCAGATAAACCAAAAAGCATGCCTAATAGAAAACCTGCTAAGAAGAATAAAAGC
CAAAAAAAGAATACTGTAACTTTCTTGAAGTAGTGGAAAGTTGGGGACAAATGTCCTGCCATTTGGTCAGAAGACAGCTG
CATTTACTCTGCTACCATTGCTTCAGTTGATATGAAGAGAGAAAGCTGTGTTGTGATTTACACTGGATATGGAAATAGAG
AGGAGCAAATCTGTCTGATTTACTTTCTTCAACCTCTGTAGCTAATAATATAGGACAGAATGCTCAAAAGAATGAAAATG
AAAGTCAAGATTCAATGGATGAAAGTGAGAACTCCAGGTCC

Alignment

ORF - retro_ptro_2813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.43 %
• Parental protein coverage: 58.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMSSGGSGGGVPEQEDSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP
          MAM.S..S..G..EQED.V.F....GQSD.SDIWD.TALI...DKAVASFK.ALKN.DICETS.KPK..P
Retrocopy MAMGSASSVCGILEQEDLVHF*CSIGQSDVSDIWDATALIEVDDKAVASFKQALKNDDICETSDKPKSMP

Parental  KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQ-NLS
          .RKPAKKNKSQKKNT...L..WKVGDKC.AIWSED.CIY.ATIAS.D.KRE.CVV.YTGYGNREEQ.NLS
Retrocopy NRKPAKKNKSQKKNTVTFLK*WKVGDKCPAIWSEDSCIYSATIASVDMKRESCVVIYTGYGNREEQ<NLS

Parental  DLLSPICEVANNIEQNAQENENESQVSTDESENSRS
          DLLS....VANNI.QNAQ.NENESQ.S.DESENSRS
Retrocopy DLLSS-TSVANNIGQNAQKNENESQDSMDESENSRS

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	0.04 RPM	8.83 RPM
SRP007412_cerebellum	0.00 RPM	13.26 RPM
SRP007412_heart	0.00 RPM	6.18 RPM
SRP007412_kidney	0.00 RPM	8.53 RPM
SRP007412_liver	0.00 RPM	9.43 RPM
SRP007412_testis	0.00 RPM	18.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2813 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2813 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4140
Gorilla gorilla	retro_ggor_2780

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813 ,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,