RetrogeneDB ID: retro_ptro_1903

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:88635917..88637351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSPTRG00000016080
• Aliases: None
• Description: Amidophosphoribosyltransferase [Source:UniProtKB/TrEMBL;Acc:H2QPI4]

Sequence

>retro_ptro_1903
CTGCAGCGCCGGGGTCAGGAGAGTGCTGGTATTCTGACTAGTGAGGGGAGTTCAGTGCCAACATTCAAATCACACAAGGG
AATGGGTCTTGTAAATCACGTCTTTACTGAAGACAATTTGAAAAAATTACATGTTTCAAATCTTGGAATTGGACACACAA
GGTATGCCGCCACAGGAAAATGTGAATTAGAAAATTGTCAGCCCTTTGTTGTTGAAACACTTCATGGGAAGATAGCTGTG
GCACATAATGGCGAATTGGCAAATGCTGCTCGATTAAGGAAAAAGCTTCTGCGTCACGGTATTGGTCTGTCCACAAGTTC
TGATAGTGAAGTGATTACCCAGTTACTGGCGTATACCCCTCCTCAGGAACAAGATGACACCCCAGACTGGGTAGCCAGGA
TTAAAAACTTGATGAAGGAAACACCCACAACATACTCCCTGCTTAAAATGCCCAGAGATGTTATTTACGCAGTATGAGAT
CATTATGGAAATCGTCCCCTATGCATTGATCGTCTTATTCCAGCGTCTGATATAAATGACAAAGAGAAAAAAACATCGGA
AACAGAAGGATGGCTGGTGTCTTCAGAATCTTGTAGCTTCTTATCTATTGGTGCAAGATATTACCGTGAAGTCTTGCCTG
GAGAAATTGTGGAAATATCCAGACGTAATGTCCGAACTCTTGATATTATATCAAGGTCTGAAGGAAACCCTATGGCTTTT
TGTATCTTTGAATATGTTTATTTTGCAAGACCAGACAGTATGTTTGAAGACCAAATGGTTTATACAATAAGATACCGTTG
TGGCCGGCAGCTAGCTATTGAAGCACCTATGGATGCAGATTTGGTTAGCACTGTTCCAGAATCTGCTACGCCTGCTGCTC
TTGCTTATGCAGGAAAGTGTGGACTTCCATATGTGGAGGTGCTGTGTAAAACCTGATATGTAGGGAGAACCTTCATTCAG
CCAAACATGAGGGTAAGACAACTTGGTGTTGCAAAAAAATTTGGAGTATTGTCAGACAACTTTAAAGGCAAAAGAATTGT
TCTTGTAGATGATTCAATTGTGAGAGGCAATACCATCTCAACTATAATAAAATTGCTCAAAGAATCTGGTGCAAAAGAGG
AACACATTCGAGTAGCTTCACCACCAATTAAATATCCATGCTTCATGGGAATAAACATTCCTACAAAAGAAGAGCTCATT
GCCAATAAACCAGAATTTGATCACCTTGCAGAATATCTAGGAGCAAACAGTGTTGTGTATCTGTCAGTAGAAGGACTGGT
TTCACCTGTACAAGAAGGGATAAAGTTTAAAAAACAGAAAGAGAAAAAGCACGATATTATGATCCAAGAAAATGGAAATG
GTCTGGAATGTTTTGAAAAGAGTGGTCATTGTACAGCTTGTCTCACTGGAAAATATCCTGTAGAATTAGAATGG

Alignment

ORF - retro_ptro_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.14 %
• Parental protein coverage: 92.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQHRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDNLKKLYVSNLGIGHTRYATTGKCELENCQPFV
          LQ.RGQESAGI.TS.GSSVPTFKSHKGMGLVNHVFTEDNLKKL.VSNLGIGHTRYA.TGKCELENCQPFV
Retrocopy LQRRGQESAGILTSEGSSVPTFKSHKGMGLVNHVFTEDNLKKLHVSNLGIGHTRYAATGKCELENCQPFV

Parental  VETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKE
          VETLHGKIAVAHNGEL.NAARLRKKLLRHGIGLSTSSDSE.ITQLLAYTPPQEQDDTPDWVARIKNLMKE
Retrocopy VETLHGKIAVAHNGELANAARLRKKLLRHGIGLSTSSDSEVITQLLAYTPPQEQDDTPDWVARIKNLMKE

Parental  APTAYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSDINDKEKKTSETEGWVVSSESCSFLSIGARYYRE
          .PT.YSLL.M.RDVIYAV.D.YGNRPLCI.RLIP.SDINDKEKKTSETEGW.VSSESCSFLSIGARYYRE
Retrocopy TPTTYSLLKMPRDVIYAV*DHYGNRPLCIDRLIPASDINDKEKKTSETEGWLVSSESCSFLSIGARYYRE

Parental  VLPGEIVEISRHNVQTLDIISRSEGNPMAFCIFEYVYFARPDSMFEDQMVYTVRYRCGQQLAIEAPVDAD
          VLPGEIVEISR.NV.TLDIISRSEGNPMAFCIFEYVYFARPDSMFEDQMVYT.RYRCG.QLAIEAP.DAD
Retrocopy VLPGEIVEISRRNVRTLDIISRSEGNPMAFCIFEYVYFARPDSMFEDQMVYTIRYRCGRQLAIEAPMDAD

Parental  LVSTVPESATPAALAYAGKCGLPYVEVLCKNRYVGRTFIQPNMRLRQLGVAKKFGVLSDNFRGKRIVLVD
          LVSTVPESATPAALAYAGKCGLPYVEVLCK..YVGRTFIQPNMR.RQLGVAKKFGVLSDNF.GKRIVLVD
Retrocopy LVSTVPESATPAALAYAGKCGLPYVEVLCKT*YVGRTFIQPNMRVRQLGVAKKFGVLSDNFKGKRIVLVD

Parental  DSIVRGNTISPIIKLLKESGAKEVHIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVY
          DSIVRGNTIS.IIKLLKESGAKE.HIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVY
Retrocopy DSIVRGNTISTIIKLLKESGAKEEHIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVY

Parental  LSVEGLVSSVQEGIKFKKQKEKKHDIMIQENGNGLECFEKSGHCTACLTGKYPVELEW
          LSVEGLVS.VQEGIKFKKQKEKKHDIMIQENGNGLECFEKSGHCTACLTGKYPVELEW
Retrocopy LSVEGLVSPVQEGIKFKKQKEKKHDIMIQENGNGLECFEKSGHCTACLTGKYPVELEW

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	6.20 RPM
SRP007412_cerebellum	0.00 RPM	7.46 RPM
SRP007412_heart	0.00 RPM	1.52 RPM
SRP007412_kidney	0.00 RPM	3.58 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.11 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1903 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1903 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2809
Gorilla gorilla	retro_ggor_1953

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023644	2 retrocopies	retro_ecab_1113, retro_ecab_270,
Homo sapiens	ENSG00000128059	1 retrocopy	retro_hsap_2809,
Gorilla gorilla	ENSGGOG00000004608	1 retrocopy	retro_ggor_1953,
Monodelphis domestica	ENSMODG00000020693	1 retrocopy	retro_mdom_1487,
Nomascus leucogenys	ENSNLEG00000008762	1 retrocopy	retro_nleu_431,
Pongo abelii	ENSPPYG00000029568	1 retrocopy	retro_pabe_2306,
Pan troglodytes	ENSPTRG00000016080	1 retrocopy	retro_ptro_1903 ,
Tursiops truncatus	ENSTTRG00000010928	1 retrocopy	retro_ttru_794,