RetrogeneDB ID: retro_ptro_670

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:16812990..16813682(+)
• 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_670
ATGGCCCCTCTGCGCTCCAGCTGTGTCCTCTCCGGGATCGCTGCCGCCTTCCACCCGGGCTCGCCTCTGATGCCCCTGCC
AGAGCCAGCTCCTGGTGGACCCATGTGGAGATGGGACCACCAGAACCCATCCTTGGAGTCACCGAAGACTTTAAGAGGGA
CACCAATAGCAAAAAGATGAATCTGGGAGTTAGTGCCTACAGGGACCACAACGGAAAGCCTTACAGCATCCACAAGGCAG
AGGCCCAGATTGCAGCCAAAAATTTGGACGAGGACTACCTCTCCATTGGGCGGCTGGCTGAATTTTGCAAGGCATCTGCA
GAAGTAGCCTTGGGCGAGAACAGCGAAGTCTCGAAAAGTGGCCGGTTTGTCACTGTGCAGACCATTTCTGGAACTAGTGC
CTTAAGGATCAGAGCCAGTTTTCTGCAAAGATTTCTTAAGTTCAGCCAAGATGTCTTTCTGCCCAAACCAACCTGGGGAA
ATCGCACACCCATCTTCAGGGATACTGGCATGCAGCTACAAGGTTATCGATACTATGACCGCAAGACTTGCGGTTTTGAC
TTCACAGGCACTGTGGAGGACATTTCAAAAACACCAGAGCAAAGTCGTCTTCTTCTGCATGCTTGCGCCCATAATCCCAC
AGGAGTGGACCCTGGTCCCAAGCAGCAGAAGGAAATAGCAACAGTGGTGAAG

Alignment

ORF - retro_ptro_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.26 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLHSGRVLPGIAAAFHPG-LAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRD
          MA.L.S..VL.GIAAAFHPG.LA..A.ARASSWWTHVEMGPP.PILGVTE.FKRDTNSKKMNLGV.AYRD
Retrocopy MAPLRSSCVLSGIAAAFHPG<LASDAPARASSWWTHVEMGPPEPILGVTEDFKRDTNSKKMNLGVSAYRD

Parental  DNGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALR
          .NGKPY...S..KAEAQIAAKNLD..YL.IG.LAEFCKASAE.ALGENSEV.KSGRFVTVQTISGT.ALR
Retrocopy HNGKPY---SIHKAEAQIAAKNLDEDYLSIGRLAEFCKASAEVALGENSEVSKSGRFVTVQTISGTSALR

Parental  IGASFLQRFFKFSRDVFLPKPTWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFTGAVEDISKIPEQSVLLL
          I.ASFLQRF.KFS.DVFLPKPTWGN.TPIFRD.GMQLQGYRYYD.KTCGFDFTG.VEDISK.PEQS.LLL
Retrocopy IRASFLQRFLKFSQDVFLPKPTWGNRTPIFRDTGMQLQGYRYYDRKTCGFDFTGTVEDISKTPEQSRLLL

Parental  HACAHNPTGVDPRPEQWKEIATVVK
          HACAHNPTGVDP.P.Q.KEIATVVK
Retrocopy HACAHNPTGVDPGPKQQKEIATVVK

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	138.46 RPM
SRP007412_cerebellum	0.00 RPM	112.85 RPM
SRP007412_heart	0.00 RPM	262.90 RPM
SRP007412_kidney	0.00 RPM	113.84 RPM
SRP007412_liver	0.07 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_670 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_670 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_971
Pongo abelii	retro_pabe_823

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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,