RetrogeneDB ID: retro_rnor_2695

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:77136801..77138079(+)
• Located in intron of: ENSRNOG00000042609

Retrocopy information

• Ensembl ID: ENSRNOG00000045714
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Got2
• Ensembl ID: ENSRNOG00000011782
• Aliases: Got2, ASPATA
• Description: Aspartate aminotransferase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00507]

Sequence

>retro_rnor_2695
CTCCTGCACTCCAGTTGCGTCCTTTCCAAGATGGCCACTGCCTTTCACCCAGGCCTTGCAGCTGCAGCCTCTGTCAGAGC
CAGCTCCTGGTGGGCCCATGTTGAGATGGAACCTCCAGATCCCATCCTGGGAGTTTCTGAAGCCTTCAAGAGAGATGCCG
GCAGCAAGAAGGTGAACCTGGAAGTTGGTGTCTACCGGGATGATAACGGAAAGCCTTACGTGCTCCCCAGTGTCTAGAAC
GCAGAGGCCCAGATTGCTGGAAAAAAAATTGGACAAAGAATACCTGCCCATTGGGGGTCTGGCTGAATTTTGTAAGGCTT
CCGCAAAACTGGCCCTGGGCGAGAACAACGAAGTGTTGAAAAGCTGCCGGTTTGTTACTGTGCAGATCATTTCTGGGACT
GGAGCCTTAAGGGTCGGAGCCAGTTTTCTGCAAAGATTTTATTGAGTTCAGCCGAGATGTCTTTCTGCACAAACCATCCT
GGGGAAGTCACACACCCATCTTCAGGGATGCCGGCATGCAGCTACAAGGTTATGGATACTATGACTCCCAAGACTTGAGG
CTTTGACTTGTCCGGAGCCTTAGAAGACTATCAAAAATCCCAGAGTAGAGTGTTCTCCTGCGTGCCTGCACTTACAACCC
CATAGGCATGGACCTGCGTCCAGAGCAGTGGAAGGAAATGGCGTCGGTGGTGAAGGAAAAGAATCTCTTCACATTCTTCG
ACATGGCCTACCAAGGCTTTGCCAATGGTGATGGTGATAAGGACGCCTGGACCGTGAGGCACTTCATCCAGCAGGGCTTA
ATGTCTGCCTCTGCCAATCATAGGCCAAGAACATGGGCCTGTACGGTGGGCATGTGGGAGCCTTCACCGTGGTCTGCAAA
GATGCGGAAGAAGCCAAAAGGGTGGAGCCACAGCTGAAGATCCTGATCCGCCCCTTGTATTCCAGCCCGCCTCTCAGTGG
AGCCTGGATCGCTGCAACCATCCTGACTTCTCCAGACTCGCAAAAGCAATGGTTGCAAGAGGTGAAAGGCATGGCTGACC
GCATCATCAGCATGAGGACCCAGCTGGTCTCCAACCTGAAGAAAGAGGGCTCATCCCACTTCAATCATGAAGTGACCAGA
TCGGCGCGTTCTGTTTCACCGGCCTAAAGCCTGAGCAAGTGAAGCGGCTGACCAAGGAGTTCTCAGTCTACATGACAAAG
GACGGCCGGATCTCCGTGGCAGGGGTCACCTCTGGCAATGTGGGCTACCTTGCCCATGCCATTCACTAGGTCACCAGG

Alignment

ORF - retro_rnor_2695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.41 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LLHSGRVLSGMAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNG
          LLHS..VLS.MA.AFHPGLAAAAS.RASSWW.HVEM.PPDPILGV.EAFKRD..SKK.NL.VG.YRDDNG
Retrocopy LLHSSCVLSKMATAFHPGLAAAASVRASSWWAHVEMEPPDPILGVSEAFKRDAGSKKVNLEVGVYRDDNG

Parental  KPYVLPSVRKAEAQIAGKN-LDKEYLPIGGLADFCKASAELALGENSEVLKSGRFVTVQTISGTGALRVG
          KPYVLPSV..AEAQIA....LDKEYLPIGGLA.FCKASA.LALGEN.EVLKS.RFVTVQ.ISGTGALRVG
Retrocopy KPYVLPSV*NAEAQIAXXX>LDKEYLPIGGLAEFCKASAKLALGENNEVLKSCRFVTVQIISGTGALRVG

Parental  ASFLQRFF-KFSRDVFLPKPSWGNHTPIFRDAGMQLQGYRYYD-PKTCGFDFSGALED-ISKIPEQSVLL
          ASFLQRF...FSRDVFL.KPSWG.HTPIFRDAGMQLQGY.YYD.PKT.GFD.SGALED..SKIPE.SVLL
Retrocopy ASFLQRFY>EFSRDVFLHKPSWGSHTPIFRDAGMQLQGYGYYD>PKT*GFDLSGALED<LSKIPE*SVLL

Parental  LHACAHNPTGVDPRPEQWKEMAAVVKKKNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGI-NVCLCQSY
          ..AC..NP.G.D.RPEQWKEMA.VVK.KNLF.FFDMAYQGFA.GDGDKDAW.VRHFI.QG..NVCLCQS.
Retrocopy -RACTYNPIGMDLRPEQWKEMASVVKEKNLFTFFDMAYQGFANGDGDKDAWTVRHFIQQGL<NVCLCQS*

Parental  AKNMGLYGERVGAFTVVCKDAEEAKRVESQLKILIRPLYSNPPLNGARIAATILTSPDLRKQWLQEVKGM
          AKNMGLYG..VGAFTVVCKDAEEAKRVE.QLKILIRPLYS.PPL.GA.IAATILTSPD..KQWLQEVKGM
Retrocopy AKNMGLYGGHVGAFTVVCKDAEEAKRVEPQLKILIRPLYSSPPLSGAWIAATILTSPDSQKQWLQEVKGM

Parental  ADRIISMRTQLVSNLKKEGSSHNWQHI-TDQIGMFCFTGLKPEQVERLTKEFSVYMTKDGRISVAGVTSG
          ADRIISMRTQLVSNLKKEG.S....H...DQIG.FCFTGLKPEQV.RLTKEFSVYMTKDGRISVAGVTSG
Retrocopy ADRIISMRTQLVSNLKKEG-SSHFNHE<SDQIGAFCFTGLKPEQVKRLTKEFSVYMTKDGRISVAGVTSG

Parental  NVGYLAHAIHQVTK
          NVGYLAHAIH.VT.
Retrocopy NVGYLAHAIH*VTR

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
SRP017611_brain	0.00 RPM	192.32 RPM
SRP017611_kidney	0.00 RPM	338.72 RPM
SRP017611_liver	0.00 RPM	350.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2695 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2695 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,