RetrogeneDB ID: retro_ptro_2002

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:89671189..89671846(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL19
• Ensembl ID: ENSPTRG00000012108
• Aliases: None
• Description: None

Sequence

>retro_ptro_2002
CAGTTCTTGAGTCCCTAATTCATTCCTCCAAGGGGAAGAATAAATCTTCTGAAGTTTCAAATAGGAAGAAAAGTTATGTT
AGAAAGGAGAAAAGTACTCCACATTCCAGAGTTCTATGTTGGAAGTATTCTTTGTGTTACTACAGCTGAATCATATGCCA
GTGAAAAAATCAGCCAGTTTCTGGGGATTTGCATCTAGAGATCAGGAAAAGGACTTGGGGCTACTTTTATCCTTAGGAAT
GTTATTGAAGGACAAGGTGTTAAGATTTGCTTTCAACTTTATAATCCTCGAATCCGGGAGACTCAAGTGGTCAAATGAGA
GAAATGGCTGGATGATAGCTTGCTGTAGTTACGAGATGCTTTTCCTGAATATAGCACTATTGATGTGAATATGAAGCCAG
TAGCACAAGAGCCTAGCCAAGAAGTTCCTGTTAATAAGCTGAAAGTGAAAATGAAGCCTCAGCCCTGGTCCAAATGCTGG
GACTGTCCAAATTTTAATATTTAAGGAATCATATTTGATCTTTGTTTCACTGAAGAACAAATGAAAGCAGCTTAGAAGTA
GAGACAGCTGTGGCTTGAATTTGATACGATGAGGGAATATGATGCTTCAAAAATTGAAGCTGCAATATGGGATGAAATTG
AAGCATCCAGAAAGTCC

Alignment

ORF - retro_ptro_2002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.0 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFLSPEFIPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVTTADPYASGKISQFLGICIQRSGR
          .FLSP.FIP.RGR...LKFQI.RK.MLERRKVLHIPEFYVGSIL.VTTA..YAS.KISQFLGICI.RSG.
Retrocopy QFLSP*FIPPRGRINLLKFQIGRKVMLERRKVLHIPEFYVGSILCVTTAESYASEKISQFLGICI*RSGK

Parental  GLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNMKPVVQEPNQ
          GLGATFILRNVIEGQGV.ICF.LYNPR..E.QVVK.EK.LDDSLL.LRDA.PEYST.DVNMKPV.QEP.Q
Retrocopy GLGATFILRNVIEGQGVKICFQLYNPRIRETQVVK*EKWLDDSLL*LRDAFPEYSTIDVNMKPVAQEPSQ

Parental  KVPVNELKVKMKPKPWSKRWERPNFNIKGIRFDLCLTEQQMKDAQKWNQPWLEFDMMREYDTSKIEAAIW
          .VPVN.LKVKMKP.PWSK.W..PNFNI.GI.FDLC.TE.QMK.A.K..Q.WLEFD.MREYD.SKIEAAIW
Retrocopy EVPVNKLKVKMKPQPWSKCWDCPNFNI*GIIFDLCFTEEQMKAA*K*RQLWLEFDTMREYDASKIEAAIW

Parental  KEIEASKRS
          .EIEAS..S
Retrocopy DEIEASRKS

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	9.76 RPM
SRP007412_cerebellum	0.00 RPM	5.27 RPM
SRP007412_heart	0.00 RPM	12.91 RPM
SRP007412_kidney	0.00 RPM	22.54 RPM
SRP007412_liver	0.00 RPM	14.50 RPM
SRP007412_testis	0.00 RPM	23.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2002 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2002 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2957
Gorilla gorilla	retro_ggor_2048
Pongo abelii	retro_pabe_2453

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002266	1 retrocopy	retro_eeur_485,
Homo sapiens	ENSG00000115364	1 retrocopy	retro_hsap_2957,
Gorilla gorilla	ENSGGOG00000027896	1 retrocopy	retro_ggor_2048,
Loxodonta africana	ENSLAFG00000000146	1 retrocopy	retro_lafr_472,
Myotis lucifugus	ENSMLUG00000012774	1 retrocopy	retro_mluc_1308,
Pongo abelii	ENSPPYG00000012255	1 retrocopy	retro_pabe_2453,
Pan troglodytes	ENSPTRG00000012108	1 retrocopy	retro_ptro_2002 ,
Ictidomys tridecemlineatus	ENSSTOG00000002873	1 retrocopy	retro_itri_549,
Tupaia belangeri	ENSTBEG00000016470	1 retrocopy	retro_tbel_326,