RetrogeneDB ID: retro_ptro_3097

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:25251376..25252064(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSPTRG00000004318
• Aliases: None
• Description: None

Sequence

>retro_ptro_3097
ATGAACCAAGGAGACTCAAACCCAGCAGCTATTCCGCATGCGGCAGAAGACATTCAAGGAGATGACAGATGGATGTGTCA
GCACAACAGATTTGTTTTGGACTGTAAAGACAAACAGCCTGATGTACCATTTGCGGGAGGCTCCGTGGTGCAGTTACTGC
AGCCATATGAGATATGGCGAGAGCTTTTTTCCCCACTTCATGCACTGAATTTTGGAACTGGGGGAGATACAACAAGACAT
GTTTTGTGGAGACTAAAGAACGGAGAACTGGGGAATACTAAGCCTAAGGTCATTGTTTTCTGGCTAGGAAGAAACAACCA
TGAAAATATGGCAGAAGAGGTAGCAGGTGGTATGGCGGCCATCGTACAACTTATCAACACAAGGCAGCCACAGGCCAAAA
TCATTGTATTTGATCTGTTACCTCAAGGTGAGAAACCCAACCCTTTGAGGCAAAAGAACGCCAAGGTGAACCCACTCGTC
AAGATTTCGCTGCTGAAACTTAACCGACGTGCAGCTCCTGGATACTGACAGGGGTTTCGTGCACTCCGACCGTGCCATCT
CCTGCCACGACATGTTTGATTTTCTGCATTTGACAGGAGGCGGCTACTCAAAGGTCTGCAAACCCTTGAATGAACTGATC
ATGCAGTTGTTGGAGGAAACACCTGAGGAGAAACAAACCACCATTGCC

Alignment

ORF - retro_ptro_3097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
          M.QGDSNPAAIPHAAEDIQGDDRWM.QHNRFVLDCKDK.PDV.F.G.S.VQL.Q.YEIWRELFSPLHALN
Retrocopy MNQGDSNPAAIPHAAEDIQGDDRWMCQHNRFVLDCKDKQPDVPFAGGSVVQLLQPYEIWRELFSPLHALN

Parental  FGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGLL
          FG.GGDTTRHVLWRLKNGEL.N.KPKVIV.W.G.NNHEN.AEEVAGG..AIVQLINTRQPQAKIIV..LL
Retrocopy FGTGGDTTRHVLWRLKNGELGNTKPKVIVFWLGRNNHENMAEEVAGGMAAIVQLINTRQPQAKIIVFDLL

Parental  PRGEKPNPLRQKNAKVNQLLKVSLPK-LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPL
          P.GEKPNPLRQKNAKVN.L.K.SL.K.L..VQLLDTD.GFVHSD.AISCHDMFDFLHLTGGGY.K.CKPL
Retrocopy PQGEKPNPLRQKNAKVNPLVKISLLK>LTDVQLLDTDRGFVHSDRAISCHDMFDFLHLTGGGYSKVCKPL

Parental  HELIMQLLEETPEEKQTTIA
          .ELIMQLLEETPEEKQTTIA
Retrocopy NELIMQLLEETPEEKQTTIA

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	0.04 RPM	102.19 RPM
SRP007412_cerebellum	0.00 RPM	101.27 RPM
SRP007412_heart	0.00 RPM	40.66 RPM
SRP007412_kidney	0.00 RPM	55.42 RPM
SRP007412_liver	0.00 RPM	33.72 RPM
SRP007412_testis	0.00 RPM	69.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3097 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3097 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4661
Gorilla gorilla	retro_ggor_2893
Pongo abelii	retro_pabe_3621
Macaca mulatta	retro_mmul_2481

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097 , retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,