RetrogeneDB ID: retro_ptro_354

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:151600336..151601422(-)
• 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_354
GATGATAACGGGAAGCCGTACATGCTGCCTAGTGTGCTCAAGGCAGAGGCCCAGATTGCTGCAAAAAATTTGGACAAGGA
ATCCCTGCCAGTAGGGGGACCGGCTGAATTTTGCAAGGCATCTGTAGAACCAACCCTGGGTGAAAACAGCAAAGTCTTGA
AAAGCGGCCGGTTTGTCACTGTGCAGACCATTTCTGGAACTGGGGCCTTAAGGATCGGAGCCAGTTTTCTCTAAAGATAT
TTTAAGTTCAGCTGAGATGTCTTTCTACCGAAACCAAGCTGGGTAAATCACACACCCATCTTCAGGGACGCTAGCATGCA
GCTACAATGTTATCGGTATTATGACCCCAAGACTTGCAGTTTTGACTTCACAGGCGCTGTGGATGACTTTTAAAACATAC
TAGAGCAAAGTGTTCTTCTCCTGCATGCCTGCACCCACAATCCCATGGGAGTGGACCCACGCCCAGAACAGTGGAAGGAA
ATAGCAACAGTTGTGAAGAAAAGGAATCTCTTTGCACTCTTTGACATGGCCTACCAAGGCTTTGCCAGTGGTGATGGTGA
TAAGGATGCCTGGGCTCTGCACCACTTCATCGAACAGGGCATTAATGTTTGTCTCTGCCAATCATATGCCAAGAACATGG
GCTTATATGGTGAGCATGTAGGAGCCTTCACTGTGGTCTGCCAAGATGCAGATGAAGCCAAAAGGGTAGAGTCACAGTTG
AAGATCTTGATTAGTCCCATGTATTCCAACTCTCCCCTCAATGGGGCCCAGATTGCTTCTACCATTCCAAACACCCCAGG
TTTGTGAAAACAATGGTTGTAAGAAGTGAAAGGCATGGCCGACTGCATCATTAGCATGCGGACTCAGCTGGTCTTCAACC
TCAAGAAGAAGGGTTCCACTCACAACCGGCAACACATCACTGACCAAATTGGCATGTCTTGTTTCACAGAGCTAAAGCCT
GAACAGGTGGGGTGGCTGACCAAGGAGTTCTCCATCTACATGACAAAGGACGGCCGCATCTCTGTGGCAGGGGTCACCTC
CAGCAACATGGGCTACCTTGCCCATGCCATTCACCAGGTCACCAAG

Alignment

ORF - retro_ptro_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.19 %
• Parental protein coverage: 84.19 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGAL
          DDNGKPY.LPSV.KAEAQIAAKNLDKE.LP.GG.AEFCKAS.E..LGENS.VLKSGRFVTVQTISGTGAL
Retrocopy DDNGKPYMLPSVLKAEAQIAAKNLDKESLPVGGPAEFCKASVEPTLGENSKVLKSGRFVTVQTISGTGAL

Parental  RIGASFLQRFFKFSRDVFLPKPTWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFTGAVEDISKIPEQSVLL
          RIGASFL.R.FKFS.DVFLPKP.W.NHTPIFRDA.MQLQ.YRYYDPKTC.FDFTGAV.D...I.EQSVLL
Retrocopy RIGASFL*RYFKFS*DVFLPKPSWVNHTPIFRDASMQLQCYRYYDPKTCSFDFTGAVDDF*NILEQSVLL

Parental  LHACAHNPTGVDPRPEQWKEIATVVKKRNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSYA
          LHAC.HNP.GVDPRPEQWKEIATVVKKRNLFA.FDMAYQGFASGDGDKDAWA..HFIEQGINVCLCQSYA
Retrocopy LHACTHNPMGVDPRPEQWKEIATVVKKRNLFALFDMAYQGFASGDGDKDAWALHHFIEQGINVCLCQSYA

Parental  KNMGLYGERVGAFTMVCKDADEAKRVESQLKILIRPMYSNPPLNGARIAAAILNTPDLRKQWLQEVKGMA
          KNMGLYGE.VGAFT.VC.DADEAKRVESQLKILI.PMYSN.PLNGA.IA..I.NTP.L.KQWL.EVKGMA
Retrocopy KNMGLYGEHVGAFTVVCQDADEAKRVESQLKILISPMYSNSPLNGAQIASTIPNTPGL*KQWL*EVKGMA

Parental  DRIIGMRTQLVSNLKKEGSTHNWQHITDQIGMFCFTGLKPEQVERLIKEFSIYMTKDGRISVAGVTSSNV
          D.II.MRTQLV.NLKK.GSTHN.QHITDQIGM.CFT.LKPEQV..L.KEFSIYMTKDGRISVAGVTSSN.
Retrocopy DCIISMRTQLVFNLKKKGSTHNRQHITDQIGMSCFTELKPEQVGWLTKEFSIYMTKDGRISVAGVTSSNM

Parental  GYLAHAIHQVTK
          GYLAHAIHQVTK
Retrocopy GYLAHAIHQVTK

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	0.14 RPM	112.85 RPM
SRP007412_heart	0.09 RPM	262.90 RPM
SRP007412_kidney	0.00 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_354 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_354 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_473
Gorilla gorilla	retro_ggor_449

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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,