RetrogeneDB ID: retro_ptro_240

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:183016305..183016722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf45
• Ensembl ID: ENSPTRG00000005381
• Aliases: None
• Description: chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]

Sequence

>retro_ptro_240
ATAGAAGTCACCACAAGCCCCAGGCCAGCTCAAGCTCTGTGTTGTCCACCCAGGACTGCTACAGAGGGAGCCTTGGTGCC
TAAGGAGTGGCTGACGGTAGGGAACAACAGCCAAGGAGGTATATCAGACAGGTTGCTCATCAACTCCCAGCTTGATTCTA
GAAAGAACTCCACTCTCCAACCAGTCCAGACACAGAGGAGTCCCTTAGTGGACCAAGGACAGACCTTTCTCCCACAGATG
GCCCAGGCACATGAAAAGCTAAGAAAATAAATGGCGGGTTCACCACCTGGTTGTTTCAATATTGAAAATATTGATGGTTC
TCTTAGAAAAGTTATACAAATGGATATGGTCTTGTTTGAGATGAACCAGTCGAATTCAAAAGTGAAGAGTTCAGAATCTG
AGGATGAAGATGACAGC

Alignment

ORF - retro_ptro_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.43 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVHGKPQ-ASPSCSSPTRDSSGVPVSKELLTAGSDGRGGIWDRLLINSQPKSRKTSTLQTVRIERSPLL
          .EV...P..A...C..P.....G..V.KE.LT.G....GGI.DRLLINSQ..SRK.STLQ.V...RSPL.
Retrocopy IEVTTSPRPAQALCCPPRTATEGALVPKEWLTVGNNSQGGISDRLLINSQLDSRKNSTLQPVQTQRSPLV

Parental  DQVQTFLPQMARANEKLRKEMAAAPPGRFNIENIDGPHSKVIQMDVALFEMNQSDSKEVDSSEESSQDS
          DQ.QTFLPQMA.A.EKLRK.MA..PPG.FNIENIDG...KVIQMD..LFEMNQS.SK...S..E...DS
Retrocopy DQGQTFLPQMAQAHEKLRK*MAGSPPGCFNIENIDGSLRKVIQMDMVLFEMNQSNSKVKSSESEDEDDS

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	2.07 RPM
SRP007412_cerebellum	0.00 RPM	1.68 RPM
SRP007412_heart	0.03 RPM	1.78 RPM
SRP007412_kidney	0.16 RPM	2.59 RPM
SRP007412_liver	0.00 RPM	5.83 RPM
SRP007412_testis	0.11 RPM	1.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_240 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_240 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_292
Gorilla gorilla	retro_ggor_331
Pongo abelii	retro_pabe_382
Macaca mulatta	retro_mmul_551

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240 ,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105, retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,