RetrogeneDB ID: retro_ptro_3104

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:38293449..38293915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSMO1
• Ensembl ID: ENSPTRG00000016574
• Aliases: MSMO1, SC4MOL
• Description: None

Sequence

>retro_ptro_3104
ATGGCAACAAATGAAAGTGCCAGCATCTGTAGTTCAGCATTTGTAGCTGTGGAGTATGTAGATTCACTTTTACCTGACAG
TCCTCTGCAAGAACCATTTTAAAATGCTTGGAATTGTATGTTAATAATTATGCAATGTTCTAGATTGCAACATGGGGATC
TGCTATTGTTCATGAAAACTTTTATTTCTTGTTCTTTTTACCTGGGTTCCTATTTCAATTTATACCTTGCATTAAAAAGA
ATAACATTGAAAAATATAAACCAGAGACATAGGAAAACCAATGGAAGTGCTTTAAATTACTTCTCTTTAATCACTTTTAT
ATCCAGCTGCTTTTATGTGTGGAACCTATTATTTTACAGAGTATTTCAATATTCTTTATGATTGAAAAAGAATGACAAAA
TGGTATATGCTTTTGGTAAGGTGCTTTGGCTATACTACAGTCTTTGATACTACTTGGCACTATTTC

Alignment

ORF - retro_ptro_3104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 52.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATNESVSIFSSASLAVEYVDSLLPENPLQEPFKNAWNYML-NNYTKFQIATWGSLIVHEALYFLFCLPG
          MATNES.SI.SSA..AVEYVDSLLP..PLQEPF.NAWN.ML.NNY..F.IATWGS.IVHE..YFLF.LPG
Retrocopy MATNESASICSSAFVAVEYVDSLLPDSPLQEPF*NAWNCML<NNYAMF*IATWGSAIVHENFYFLFFLPG

Parental  FLFQFIPYMKKYKIQKDKPETWENQWKCFKVLLFNHFCIQLPL-ICGTYYFTEYFNIPYDWERMPRWYFL
          FLFQFIP..KK..I.K.KPET.ENQWKCFK.LLFNHF.IQL.L..CGTYYFTEYFNI.YD..RM..WY.L
Retrocopy FLFQFIPCIKKNNIEKYKPET*ENQWKCFKLLLFNHFYIQLLL<MCGTYYFTEYFNILYD*KRMTKWYML

Parental  LARCFG-CAVIEDTWHYF
          L.RCFG...V...TWHYF
Retrocopy LVRCFGYTTVFDTTWHYF

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	21.86 RPM
SRP007412_cerebellum	0.00 RPM	7.24 RPM
SRP007412_heart	0.00 RPM	1.54 RPM
SRP007412_kidney	0.00 RPM	23.59 RPM
SRP007412_liver	0.00 RPM	48.58 RPM
SRP007412_testis	0.00 RPM	7.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3104 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005596	1 retrocopy	retro_amel_447,
Choloepus hoffmanni	ENSCHOG00000007550	2 retrocopies	retro_chof_1657, retro_chof_560,
Callithrix jacchus	ENSCJAG00000009301	1 retrocopy	retro_cjac_2245,
Felis catus	ENSFCAG00000023004	1 retrocopy	retro_fcat_863,
Homo sapiens	ENSG00000052802	1 retrocopy	retro_hsap_4672,
Gorilla gorilla	ENSGGOG00000015730	1 retrocopy	retro_ggor_2898,
Loxodonta africana	ENSLAFG00000007061	1 retrocopy	retro_lafr_570,
Macaca mulatta	ENSMMUG00000012994	1 retrocopy	retro_mmul_2486,
Nomascus leucogenys	ENSNLEG00000006501	1 retrocopy	retro_nleu_2164,
Oryctolagus cuniculus	ENSOCUG00000003769	1 retrocopy	retro_ocun_1454,
Otolemur garnettii	ENSOGAG00000009281	2 retrocopies	retro_ogar_182, retro_ogar_3404,
Pan troglodytes	ENSPTRG00000016574	1 retrocopy	retro_ptro_3104 ,
Pteropus vampyrus	ENSPVAG00000013707	4 retrocopies	retro_pvam_1405, retro_pvam_550, retro_pvam_598, retro_pvam_784,
Sorex araneus	ENSSARG00000013546	1 retrocopy	retro_sara_635,
Sarcophilus harrisii	ENSSHAG00000000135	1 retrocopy	retro_shar_530,
Tursiops truncatus	ENSTTRG00000012897	2 retrocopies	retro_ttru_20, retro_ttru_801,