RetrogeneDB ID: retro_pabe_3640

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:56575633..56576331(+)
• 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_3640
TCCTGGTGGACCTGTGTGGAGATGGGACTTCCAGATCCTATCCTGGGAGTCACCAAAGCCTTTAAGAGAGACACCGATAG
CAAAAAGATGAATCTGGGAGTTTGTGTCTACTGGGATGATAATGGAAAGCCTTACATGCTGCTTAATGTCAACAAGGAAG
AGGCCCAGATTGCCACAGAAAATTTGGACAAAGAATACCTGCCCATTGGGGGACTGGCTGAATTTTGCACGGCATCTGCA
GAACTAGCCTGGGTGAGAATAGTGAAGTGTTGAAAAATGTCTGGTTATTCACTGTGCATACCATTTCTGGAACTGCGACC
TTAAGGATCAGAGCCAGTTTTCTGCAAAGATTTTTTAAGCTCAGCCAGGATGTCCAAACCATCCTGGGGAAATCACACAC
CCATCTTCAGGGATGCTGGCATGCAGCTACAAATTTATTGTTACTACAACCCCAAGACTTGGTGTTTGACTTCACAGGTC
GTATGGAGGACATTTCAAAAATACCAGAGCAAAGGGTTTTTCTGTATGTCTGTGCCCATAATCCCATGGGAGTGGAACCT
CGTCTAGAGCAGTGGAAGGAAATAGCAACAGTGGTGAAGAAAAATAATCTCTTTGCATTCTTTGACATGGCCTAGCAAGG
GTTTGCTAGTGATGATTGTAACAAGGATGCCTGGGCTGTGCGCCACTTCATCAAACAG

Alignment

ORF - retro_pabe_3640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIG
          SWWT.VEMG.PDPILGVT.AFKRDT.SKKMNLGV..Y.DDNGKPY.L..V.K.EAQIA..NLDKEYLPIG
Retrocopy SWWTCVEMGLPDPILGVTKAFKRDTDSKKMNLGVCVYWDDNGKPYMLLNVNKEEAQIATENLDKEYLPIG

Parental  GLAEFCKASAELA-LGENSEVLKSGRFVTVQTISGTGALRIGAS-FLQRFFKFSRDVFLPKPSWGNHTPI
          GLAEFC.ASAELA.LGENSEVLK.....TV.TISGT..LRI.AS.F...F....R.....KPSWGNHTPI
Retrocopy GLAEFCTASAELA<LGENSEVLKNVWLFTVHTISGTATLRIRAS>FCKDFLSSAR---MSKPSWGNHTPI

Parental  FRDAGMQLQGYRYYDPKT-CGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRN
          FRDAGMQLQ.Y.YY.PKT...FDFTG..EDISKIPEQ.V.L...CAHNP.GV.PR.EQWKEIATVVKK.N
Retrocopy FRDAGMQLQIYCYYNPKT<LVFDFTGRMEDISKIPEQRVFL-YVCAHNPMGVEPRLEQWKEIATVVKKNN

Parental  LFAFFDMAYQGFASGDGDKDAWAVRHFIEQ
          LFAFFDMA.QGFAS.D..KDAWAVRHFI.Q
Retrocopy LFAFFDMA*QGFASDDCNKDAWAVRHFIKQ

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	0.09 RPM	165.27 RPM
SRP007412_kidney	0.10 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_3640 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3640 has 0 orthologous retrocopies within eutheria group .

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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,