RetrogeneDB ID: retro_ptro_837

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:86014732..86015185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOBKL1B
• Ensembl ID: ENSPTRG00000012079
• Aliases: MOBKL1B, MOB1A, MOBK1B
• Description: None

Sequence

>retro_ptro_837
ATGGATCACATGCAACAATGTGGATTTTTCTACCAGAATATTAAGGAATTATCTCCTGGAGCAAGCCGTCCAGTCGTGTC
TGCATATCCAAAATATAAATATTATTTGGCAGGTGATATTAACATTAAAAAGCTAATCAAATATACTCTTCTAAAATGCA
TGCGTTATTTTGATGACTTTGGTTCTAAATCAGCTTGATGATACTCATTTTCCTTCTAAGATTACAATCCCATTTCCCAA
AATCTTTGTAACAAAGCCTATTTATTCTCAAGTGTTTGTTTAGGGTTTATACCTGTATTTATCAGCAGCACATTGATTCT
GTGATGCAAAAGCAGAGGAAGCCCACTTCAACACTTTCTTAAGTACTTAATTTTCTTTGTTTAAGAGCTCAATCTGACTG
ATAAGGATGAGTTGACACCTCTTCAGGAATTAATTGAGAAGCTTGGAACAAAG

Alignment

ORF - retro_ptro_837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.41 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VDFFNQINMLYGTITEFCTEASCPVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDY-LMTWVQDQLDDET
          .D...Q....Y..I.E....AS.PV.SA.P.Y.Y..A...NIKK.IK....K...Y.LMT.V..QLDD.T
Retrocopy MDHMQQCGFFYQNIKELSPGASRPVVSAYPKYKYYLAGDINIKKLIKYTLLKCMRY>LMTLVLNQLDD-T

Parental  LFPSKIGVP-FPKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQ-EEAHLNTSF-KHFIFFVQEFNLID
          .FPSKI..P.FPK........ILK.LFRVY..IY.QH.DSVMQ.Q.EEAH.NT...K..IFFV.E.NL.D
Retrocopy HFPSKITIP>FPKSL*Q-SLFILKCLFRVYTCIYQQHIDSVMQKQ<EEAHFNTFL<KYLIFFV*ELNLTD

Parental  RRELAPLQELIEKLGSK
          ..EL.PLQELIEKLG.K
Retrocopy KDELTPLQELIEKLGTK

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	0.05 RPM	5.68 RPM
SRP007412_cerebellum	0.00 RPM	7.96 RPM
SRP007412_heart	0.00 RPM	18.77 RPM
SRP007412_kidney	0.00 RPM	43.70 RPM
SRP007412_liver	0.00 RPM	12.67 RPM
SRP007412_testis	0.00 RPM	35.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_837 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_837 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1223
Gorilla gorilla	retro_ggor_954
Pongo abelii	retro_pabe_1017
Macaca mulatta	retro_mmul_1299

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007277	1 retrocopy	retro_chof_502,
Echinops telfairi	ENSETEG00000018245	1 retrocopy	retro_etel_425,
Homo sapiens	ENSG00000114978	2 retrocopies	retro_hsap_1223, retro_hsap_4670,
Gorilla gorilla	ENSGGOG00000010015	1 retrocopy	retro_ggor_954,
Loxodonta africana	ENSLAFG00000014338	2 retrocopies	retro_lafr_223, retro_lafr_285,
Macaca mulatta	ENSMMUG00000015208	2 retrocopies	retro_mmul_1299, retro_mmul_297,
Nomascus leucogenys	ENSNLEG00000000321	2 retrocopies	retro_nleu_2161, retro_nleu_694,
Otolemur garnettii	ENSOGAG00000003504	1 retrocopy	retro_ogar_2688,
Pongo abelii	ENSPPYG00000012284	2 retrocopies	retro_pabe_1017, retro_pabe_3629,
Pan troglodytes	ENSPTRG00000012079	2 retrocopies	retro_ptro_3103, retro_ptro_837 ,
Rattus norvegicus	ENSRNOG00000042657	2 retrocopies	retro_rnor_2544, retro_rnor_2545,