RetrogeneDB ID: retro_ptro_759

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:43965028..43965565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MESDC2
• Ensembl ID: ENSPTRG00000007366
• Aliases: None
• Description: None

Sequence

>retro_ptro_759
ATGGTCCTAATTCATGCCTCTGGCCTACTGCTGCAGCAGCAGCTACCTGGGGCTTGTGCAGCCAAGGGCCCAGCCAGAAC
ACCCAGTAAGGCTCTCTCACTTCCTCAGAAGAAGGAAGATATTCATGATTACAATGATATAGACATGGCATGTCTTCTGG
TAGAGTGGGAGAAGGATGATGACATAAAAAAAGATCTTCCAGAGCACAAGAGACCCTCAATACCTGTCAACTTCTTATAT
ATCAACCTGGGCAAGCCTGAAAGCACATTGAAAATGATGAAAAAGGGAAGATTCTTATATGTTTGTCACTGTATCAGGAA
CCCCACTGAGAAAGAGAGACGAAATCATGAGCCTCTGTCAGGGCAGTCTTTTCAATGCTAATGAAATGTCCAGAGGTTCA
TTGTGGGATCAGACCATACTATCTTCATGCTTCATGATGGAAAATATGCCTGGGAGATCAAGAACTCTTTCGTCAGTGAA
GACAAGTGTGCTGACGCACCTCTGGAGGGACAGGTGTTCCCTGGCAAAGGAGAAGGA

Alignment

ORF - retro_ptro_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 79.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVLLCASDLLLLLLLLPPPGSCAAEGSPGTPDESTPPPRKKKKDIRDYNDADMARLLEQWEKDDDIEEGD
          .VL..AS.LLL...L...PG.CAA.G...TP......P.KK..DI.DYND.DMA.LL..WEKDDDI...D
Retrocopy MVLIHASGLLLQQQL---PGACAAKGPARTPSKALSLPQKKE-DIHDYNDIDMACLLVEWEKDDDIKK-D

Parental  LPEHKRPSAPVDFSKIDPSKPESILKMTKK-GKTLM-MFVTVSGSPTEKETEEITSLWQGSLFNANY-DV
          LPEHKRPS.PV.F..I...KPES.LKM.KK.GK.L..MFVTVSG.P..K...EI.SL.QGSLFNAN...V
Retrocopy LPEHKRPSIPVNFLYINLGKPESTLKMMKK<GKILI<MFVTVSGTPLRKR-DEIMSLCQGSLFNANE<NV

Parental  QRFIVGSDRAIFMLRDGSYAWEIKDFLVGQDRCADVTLEGQVYPGKGGG
          QRFIVGSD..IFML.DG.YAWEIK...V..D.CAD..LEGQV.PGKG.G
Retrocopy QRFIVGSDHTIFMLHDGKYAWEIKNSFVSEDKCADAPLEGQVFPGKGEG

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	6.86 RPM
SRP007412_cerebellum	0.00 RPM	6.63 RPM
SRP007412_heart	0.03 RPM	6.56 RPM
SRP007412_kidney	0.00 RPM	11.69 RPM
SRP007412_liver	0.00 RPM	13.52 RPM
SRP007412_testis	0.00 RPM	7.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_759 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_759 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_990
Gorilla gorilla	retro_ggor_793
Callithrix jacchus	retro_cjac_3285

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007811	1 retrocopy	retro_cjac_3285,
Homo sapiens	ENSG00000117899	1 retrocopy	retro_hsap_990,
Gorilla gorilla	ENSGGOG00000027583	1 retrocopy	retro_ggor_793,
Loxodonta africana	ENSLAFG00000014513	1 retrocopy	retro_lafr_505,
Monodelphis domestica	ENSMODG00000019402	2 retrocopies	retro_mdom_30, retro_mdom_344,
Oryctolagus cuniculus	ENSOCUG00000016290	1 retrocopy	retro_ocun_1947,
Pan troglodytes	ENSPTRG00000007366	1 retrocopy	retro_ptro_759 ,