RetrogeneDB ID: retro_pabe_823

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:17105811..17106503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSPPYG00000007413
• Aliases: None
• Description: Aspartate aminotransferase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5REB0]

Sequence

>retro_pabe_823
ATAGCCCCTCTGCTCTCCAGCTGCGTCCTCTCCGGGATCGCCGCCGCCTTCCACCCGGGATCGCCTCTGATGCCCCTGCC
AGAGCCAGCTCCTGGTGGACCCGTGTGGAGATGGGGCCACCAGATCCCATCCTGGGAGTCACCGAAGCCTTTAAGAGGGA
CACCAATAGCAAAAAGATGAATCTGGGAGTTAGTGCCTACAGGGACCACAACGGAAAGCCTTACAGCATCCACAAGGCAG
AGGCCCAGATTGCAGCCAAAAATTTGGACAAGGAATACCTCTCCATTGGGCGGCTGGCTGAATTTTGCAAGGCATCTGCA
GAAGTAGCCTTGGGCGAGAACAGCAAAGTCTGGAAAAGTGGCCGGTTTGTCACTGTGCAGACCATTTCTGGAACTGGTGC
CTTAAGGATCAGAGCCAGTTTTCTGCAAAGATTTCTTAAGTTCAGCCACGATGTCTTTCTGCCCAAACCAACCTGGAGAA
ATCACACACCCATCTTCAGGGATACTGGCATGCAGCTACAAGGTTATCGATATTATGACCCCAAGACTTGCGGTTTCGAC
TTCACAGGCACTATGGAGGACATTTCAAAAATACCAGAGCAAAGTCGTCTTCTTCTGCATGCCTGCGCCCATAATCCCAC
GGGAGTGGACCCTGGTCCCAAGCAGCGGAAGGAAATAGCAACAGTGGTGAAG

Alignment

ORF - retro_pabe_823 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  MALLHSGRALPGIAAAFHPG-LAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRD
          .A.L.S...L.GIAAAFHPG..A..A.ARASSWWT.VEMGPPDPILGVTEAFKRDTNSKKMNLGV.AYRD
Retrocopy IAPLLSSCVLSGIAAAFHPG<IASDAPARASSWWTRVEMGPPDPILGVTEAFKRDTNSKKMNLGVSAYRD

Parental  DNGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALR
          .NGKPY...S..KAEAQIAAKNLDKEYL.IG.LAEFCKASAE.ALGENS.V.KSGRFVTVQTISGTGALR
Retrocopy HNGKPY---SIHKAEAQIAAKNLDKEYLSIGRLAEFCKASAEVALGENSKVWKSGRFVTVQTISGTGALR

Parental  IGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFTGAVEDISKIPEQSVLLL
          I.ASFLQRF.KFS.DVFLPKP.W.NHTPIFRD.GMQLQGYRYYDPKTCGFDFTG..EDISKIPEQS.LLL
Retrocopy IRASFLQRFLKFSHDVFLPKPTWRNHTPIFRDTGMQLQGYRYYDPKTCGFDFTGTMEDISKIPEQSRLLL

Parental  HACAHNPTGVDPRPEQWKEIATVVK
          HACAHNPTGVDP.P.Q.KEIATVVK
Retrocopy HACAHNPTGVDPGPKQRKEIATVVK

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	95.43 RPM
SRP007412_cerebellum	0.00 RPM	91.93 RPM
SRP007412_heart	0.00 RPM	165.27 RPM
SRP007412_kidney	0.00 RPM	70.04 RPM
SRP007412_liver	0.00 RPM	158.39 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_823 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_823 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_971
Pan troglodytes	retro_ptro_670

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 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,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
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,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
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,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
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,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,