RetrogeneDB ID: retro_ptro_3115

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:56663823..56664522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSPTRG00000008185
• Aliases: None
• Description: Aspartate aminotransferase [Source:UniProtKB/TrEMBL;Acc:H2QB89]

Sequence

>retro_ptro_3115
TCCTGGTGGACCTATGTGGAGATGGGACTTCCAGATCCCATCCTGGGAGTCACCAAAGCCTTTAGGAGGGACACCGATAG
CAAAAAGATGAATCTGGGAGTTTGTGTCCACTGGGATGATAATGGAAAGCCTTACATGCTGCTTAATGGCAACAAGGAAG
AGGCCCAGATTGCCACAAAAAATTTGGACAAAGAATACCTGCCCATTGGGGGTCTGGCTGAATTTTGCATGGCATCTGCA
GAACTAGCCCTGGGTGAGAATAGTGAAGTGTTGAAAAATGTCCAGTTATTCACTGTGCATACCATTTCTGGAACTGCGAC
CTTAACGATCAGAGCCTGTTTTCTGCAAAGATTTTTTAAGCTCAGCCAGGATGTCCAAACCATCCTGGGGAAATCACACA
CCCATCTTCAGGGATGCTGGCATGCAGCTACAAATTTATTGTTACTACGACCCCAAGACTTGGTGTTTGACTTCACAGGT
CATATATAGGACATTTCAAAAATACCAGAGCAAAGTGTTTTTCTGCATGCCTGTGCCCATAATCCTATGGGAGTGGAACC
TCGTCTAGAGCAGTGGAAAGAAATAGCAACAGTGGTGAAGAAAAATAATCTCTTTGCATTCTTTGACATGGCCTAGCAAG
GGTTTGCTAGTGATGATTGTAACAAGGATGCCTGGGCTGTGCACCACTTCATCAAAGAG

Alignment

ORF - retro_ptro_3115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIG
          SWWT.VEMG.PDPILGVT.AF.RDT.SKKMNLGV....DDNGKPY.L....K.EAQIA.KNLDKEYLPIG
Retrocopy SWWTYVEMGLPDPILGVTKAFRRDTDSKKMNLGVCVHWDDNGKPYMLLNGNKEEAQIATKNLDKEYLPIG

Parental  GLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALRIGAS-FLQRFFKFSRDVFLPKPTWGNHTPIF
          GLAEFC.ASAELALGENSEVLK.....TV.TISGT..L.I.A..F...F....R.....KP.WGNHTPIF
Retrocopy GLAEFCMASAELALGENSEVLKNVQLFTVHTISGTATLTIRAC>FCKDFLSSAR---MSKPSWGNHTPIF

Parental  RDAGMQLQGYRYYDPKT-CGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRNL
          RDAGMQLQ.Y.YYDPKT...FDFTG...DISKIPEQSV.L.HACAHNP.GV.PR.EQWKEIATVVKK.NL
Retrocopy RDAGMQLQIYCYYDPKT<LVFDFTGHI*DISKIPEQSVFL-HACAHNPMGVEPRLEQWKEIATVVKKNNL

Parental  FAFFDMAYQGFASGDGDKDAWAVRHFIEQ
          FAFFDMA.QGFAS.D..KDAWAV.HFI..
Retrocopy FAFFDMA*QGFASDDCNKDAWAVHHFIKE

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	0.02 RPM	138.46 RPM
SRP007412_cerebellum	0.00 RPM	112.85 RPM
SRP007412_heart	0.00 RPM	262.90 RPM
SRP007412_kidney	0.08 RPM	113.84 RPM
SRP007412_liver	0.00 RPM	156.40 RPM
SRP007412_testis	0.00 RPM	23.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3115 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3115 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115 , retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,