RetrogeneDB ID: retro_pabe_383

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:47506516..47507135(-)
• Located in intron of: ENSPPYG00000000346

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSPPYG00000008333
• Aliases: None
• Description: solute carrier family 25, member 39 [Source:HGNC Symbol;Acc:24279]

Sequence

>retro_pabe_383
CTGAGCCCTTACCTCTACATAACCTTGGTAGCTGGTGTGCTGGCCCACCCTGGCACTATCACTGCAATCATCAGTGCCCT
GGAGCTTATGCAGACAAAGCTGCAGGTTCAGCATATGTTATACTATGTGCTGGTACCTGTGTTTGAGCTCCGGTGGCTTA
GAGTGGTTGGTGCTCACTGTGGCTGTGCCGGGGCCCTACTCTCCTTTGAGATGTGCCCTTCTCAGCCCTGTACTGGTTCA
ACTACGAGTTAGTGAAGAGCTGGCTGAATGGGCTCAGACCAAAGGACCTCCATGGTCCCATGACAACCATGGGAGTCAGC
TTTGCAGCTGGCAGCATCACCATGATGCTGGCTACAGTGCTGACCCTAACCTTTGTCGTGATGAAGACTCAACACCAGGC
CACACTCGGAGTGATGGAAGCTGTGGAAATGACATCCCTGGATGTGGACTCTACCTGGTTGCTCAGAGGTGGATCTGTGC
CAAGTCGGGCATCAGAGAGCTCTTTGCAGGCTTCCTCCCTTGGATCATCAAGTCTATCCCCTCCTATGCTATCACGATCA
CCACTTATGAGTTCAGCAAAAGTCTCTTAAAGAGACTCAATCAGGACCAGCATCTGGGC

Alignment

ORF - retro_pabe_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 57.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSDLYAPMVAGALARLGTVT-VISPLELMRTKLQAQHVSYREL-GACVRTAVAQGGWRSLWLGWGPTAL
          L...LY...VAG.LA..GT.T..IS.LELM.TKLQ.QH..Y..L.G.CV...VA..GW.SLWL..GPT.L
Retrocopy LSPYLYITLVAGVLAHPGTITAIISALELMQTKLQVQHMLYYVL<GTCV*APVA*SGWCSLWLCRGPTLL

Parental  RDVPFSALYWFNYELVKSWLSGLRPKD----QTSVGMSFVAGGISGTVAAVLTLPFDVVKTQRQIALGAM
          .DVPFSALYWFNYELVKSWL.GLRPKD.....T..G.SF.AG.I....A.VLTL.F.V.KTQ.Q..LG.M
Retrocopy *DVPFSALYWFNYELVKSWLNGLRPKDLHGPMTTMGVSFAAGSITMMLATVLTLTFVVMKTQHQATLGVM

Parental  EAVRVNPLHVDSTWLL-LRRIQAESGTKGLFAGFLPRIIKAAPSCAIMISTYEFGKSFFQRLNQDRLLG
          EAV....L.VDSTWLL..R.I.A.SG...LFAGFLP.IIK..PS.AI.I.TYEF.KS...RLNQD..LG
Retrocopy EAVEMTSLDVDSTWLL<QRWICAKSGIRELFAGFLPWIIKSIPSYAITITTYEFSKSLLKRLNQDQHLG

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	0.06 RPM	31.07 RPM
SRP007412_cerebellum	0.00 RPM	19.21 RPM
SRP007412_heart	0.00 RPM	13.37 RPM
SRP007412_kidney	0.03 RPM	91.98 RPM
SRP007412_liver	0.03 RPM	41.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_383 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_383 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383 ,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,