RetrogeneDB ID: retro_pabe_2902

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:118299273..118299859(+)
• Located in intron of: ENSPPYG00000016942

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSPPYG00000004207
• Aliases: None
• Description: triosephosphate isomerase 1 [Source:HGNC Symbol;Acc:12009]

Sequence

>retro_pabe_2902
CAGAAGCTAGAGCCCAAGATTGCTGTGGCTGCGCAGAACTGCTACAAAGTAACTAACGGGGCCTTTACTGGGGAGATCAG
CCCTGGCACGATCAAAGACTACAAAGCCAGTCGAGGGTCCTGGGGCACTCAGAGAGTAGGCATGTCTTTGGGGAGTCAGA
TAAGCTGATTGGGTAGAAAGTGGCCCATGCTCTGGCAGGGGGACTCAGAGTAATCGCTTGCATTGGGGAGAAGCTAGCTG
AAAGGGAAGTGGCATCACTGAGAAGTTTGTTTTCGAGAAGAAAGAGGTCATCGCAGATAACGTGAAGGACTGGAGCAAGG
TCGTCCTGGCCTGTGAGCCTGTGTGGGCCATTGGTACCAGCAAGACTGCAACACCCCAGAAGGCCCAGAAAGTACACGAG
AAGCTCTGAGAATGGCTTAAGTCCAACGTCTCTGATGTGGTGGCTCAGAGCACCCGTATCATTTATGGAGGCTCTGTGAC
AGGGGCAACCTACAAGGAGCTGGCCAGCCAGCCTGAAGTGGATGGCTTCCTCGTGGGTGATGCTTCCCTCAAGCCCGAAT
TCGTGGACATCATCAATGTCAAACAA

Alignment

ORF - retro_pabe_2902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLG-HSERRHVFGESDELIGQKVAHALAEGL
          QKL.PKIAVAAQNCYKVTNGAFTGEISPG.IKD..A.....G.HSE.RHVFGESD.LIG.KVAHALA.GL
Retrocopy QKLEPKIAVAAQNCYKVTNGAFTGEISPGTIKDYKASRGSWG<HSESRHVFGESDKLIG*KVAHALAGGL

Parental  GVIACIGEKLDERE-AGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRG
          .VIACIGEKL.ERE..GITEK.VFE...VIADNVKDWSKVVLA.EPVWAIGT.KTATPQ.AQ.VHEKL..
Retrocopy RVIACIGEKLAERE<SGITEKFVFEKKEVIADNVKDWSKVVLACEPVWAIGTSKTATPQKAQKVHEKL*E

Parental  WLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          WLKSNVSD.VAQSTRIIYGGSVTGAT.KELASQP.VDGFLVG.ASLKPEFVDIIN.KQ
Retrocopy WLKSNVSDVVAQSTRIIYGGSVTGATYKELASQPEVDGFLVGDASLKPEFVDIINVKQ

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	472.24 RPM
SRP007412_cerebellum	0.00 RPM	295.37 RPM
SRP007412_heart	0.06 RPM	287.07 RPM
SRP007412_kidney	0.07 RPM	295.27 RPM
SRP007412_liver	0.00 RPM	271.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2902 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2902 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3510
Pan troglodytes	retro_ptro_2382
Macaca mulatta	retro_mmul_1864
Callithrix jacchus	retro_cjac_2370

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902 ,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,