RetrogeneDB ID: retro_ggor_1953

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:89198500..89199664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSGGOG00000004608
• Aliases: None
• Description: Amidophosphoribosyltransferase [Source:UniProtKB/TrEMBL;Acc:G3QPM3]

Sequence

>retro_ggor_1953
CTGCAGCGCCGGGGTCAGGAGAGTGCTGGTATTCTGACTAGTGACGGGAGTTCAGTGCCAACATTCAAATCACACGAGGG
AATGGGTCTTGTAAATCACGTCTTTACTGAAGACAATTTGAAAAAATTACATGTTTCAAATCTTGGAATTGGACACACAA
GGTATGCCACCACAGGAAAATGTGAATTAGAAAATTGTCAGCCCTTTGTTGTTGAAACACTTCATGGGAAGATAGCTGTG
GCACATAATGGCCAATTGGCAAATGCTGCTCGATTAAGGAAAAAGCTTCTGCGTCATGGTATTGGTCTGTCCACAAGTTC
TGATAGTGAAGTGATTACCCAGTTACTGGCGTATAACCCTCCTCAGGAACAAGATGACACCCCAGACTGGGTAGCCAGGA
TTAAAAACTTGATGAAGGAAACGCCCACAGCATACTCCCTGCTTAAAATGCCCAGAGATGTTACTTACGCAGTATGAGAT
CCTTATGGAAATCGTCCCTTATGCATTGATCGTCTTATTCCAGTGTCTGGTATAAATGACAAAGAGAAAAAAACATCAGA
AACAGAAGGATGGGTGGTGTCTTCAGAATCTTGTAGCTTCTTATCTGTTGGTGCAAGATTTTACCGTGAAGTCTTGCCTG
GAGAAATTGTGGAAATATCCAGACGTAATGTCCGAACTCTTGATATTATATCAAGGTCTGAAGGAAACCCTATGGCTTTT
CGTATCTTTGAATATGTTTATTTTGCAAGACCAGACAGTATGTTTGAAGACCAAATGGTTTATACAATAAGATACCGTTG
TGGCCAGCAGCTAGCTATTGAAGCTCCTGTGGATGCAGATTTGGTTAGCACTGTTCCAGAATCTGCTACACCTGCTGCTC
TTGCTTATGCAGGGAAGTGTGGACTTCCATATGTGGAGGTGCTGTGTAAAACCCGATATGTATGGAGAACCTTCATTCAG
CCACACATGAGGTTAAGACAACTTGGTGTTGCAAAAAAATTTGGAGTATTGTCAGACACCTTTAAAGGCAAAAGAATTGT
TCTTGTAGATGATTCAATTGTGAGAGGCAATACCATCTCACCTATAATAACATTGCTCAAAGAATCTGGTGCAAAAGAGG
AACACATTCGAGTAGCTTCACCACCAATTAAATATCCATGCTTC

Alignment

ORF - retro_ggor_1953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 75.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQHRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDNLKKLYVSNLGIGHTRYATTGKCELENCQPFV
          LQ.RGQESAGI.TSDGSSVPTFKSH.GMGLVNHVFTEDNLKKL.VSNLGIGHTRYATTGKCELENCQPFV
Retrocopy LQRRGQESAGILTSDGSSVPTFKSHEGMGLVNHVFTEDNLKKLHVSNLGIGHTRYATTGKCELENCQPFV

Parental  VETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKE
          VETLHGKIAVAHNG.L.NAARLRKKLLRHGIGLSTSSDSE.ITQLLAY.PPQEQDDTPDWVARIKNLMKE
Retrocopy VETLHGKIAVAHNGQLANAARLRKKLLRHGIGLSTSSDSEVITQLLAYNPPQEQDDTPDWVARIKNLMKE

Parental  APTAYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSDINDREKKTSETEGWVVSSESCSFLSIGARYYRE
          .PTAYSLL.M.RDV.YAV.DPYGNRPLCI.RLIPVS.IND.EKKTSETEGWVVSSESCSFLS.GAR.YRE
Retrocopy TPTAYSLLKMPRDVTYAV*DPYGNRPLCIDRLIPVSGINDKEKKTSETEGWVVSSESCSFLSVGARFYRE

Parental  VLPGEIVEISRHNVQTLDIISRSEGNPMAFCIFEYVYFARPDSMFEDQMVYTVRYRCGQQLAIEAPVDAD
          VLPGEIVEISR.NV.TLDIISRSEGNPMAF.IFEYVYFARPDSMFEDQMVYT.RYRCGQQLAIEAPVDAD
Retrocopy VLPGEIVEISRRNVRTLDIISRSEGNPMAFRIFEYVYFARPDSMFEDQMVYTIRYRCGQQLAIEAPVDAD

Parental  LVSTVPESATPAALAYAGKCGLPYVEVLCKNRYVGRTFIQPNMRLRQLGVAKKFGVLSDNFKGKRIVLVD
          LVSTVPESATPAALAYAGKCGLPYVEVLCK.RYV.RTFIQP.MRLRQLGVAKKFGVLSD.FKGKRIVLVD
Retrocopy LVSTVPESATPAALAYAGKCGLPYVEVLCKTRYVWRTFIQPHMRLRQLGVAKKFGVLSDTFKGKRIVLVD

Parental  DSIVRGNTISPIIKLLKESGAKEVHIRVASPPIKYPCF
          DSIVRGNTISPII.LLKESGAKE.HIRVASPPIKYPCF
Retrocopy DSIVRGNTISPIITLLKESGAKEEHIRVASPPIKYPCF

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	0.05 RPM	10.31 RPM
SRP007412_cerebellum	0.00 RPM	10.36 RPM
SRP007412_heart	0.03 RPM	0.63 RPM
SRP007412_kidney	0.00 RPM	8.34 RPM
SRP007412_liver	0.03 RPM	6.28 RPM
SRP007412_testis	0.00 RPM	27.25 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1953 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2809
Pan troglodytes	retro_ptro_1903

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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,