RetrogeneDB ID: retro_pabe_1008

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:60988213..60989024(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSPPYG00000001894
• Aliases: TARDBP, TDP43
• Description: TAR DNA-binding protein 43 [Source:RefSeq peptide;Acc:NP_001127597]

Sequence

>retro_pabe_1008
ATGTCTGAATATATTCGGGTACTGAAGATGAGAAGGATGAGCCCATTGAAATACTATCGAAAGACGATGGGACAGTGCTG
CTGTCTATGGTTACAGCCCAGTTTCCAGGGGCGTGTGGCTTTGCTACAGGAATCCAGTGTCTCAATGTATGAGAGGTGTC
CGGCTGGTAGAAGGAATTCTTCATGCCCCCGATGCTGGCTGGGGAAATCTGGTGTATGTTGTCAACTATCCCAAAGATAA
CAAAAGAAAAATGGATGAGATAGATGCTTCATCAGCAGTGAAAGTGAAAAGAGCAGTCCAGAAAACATCCGATTTAGTAG
TGTTGGGTCTCACATGGAAAACAACTGAGCAGGACCTGAAAGAATATTTTAGTACCTTTGGAGAAGTTCTTATGGTGCAG
GTCAAGAAAGATAGTAAGACTGGTCATTCAAAGAGGCTTGGCTTCATTTGTTTTATGGAAGATGAAACACAGGTGAAAGT
AATGTCACAGCTACATATGATAGATGGACGGTGGTGTGACTGTAAACTTCCCAATTCTAAGCAAAGCCCAGATAAGCCTT
TGAGAAGCATAAAAGTATCTGTGGGGCACTGAACAGAGGACATGACTGCAGATGAGCTGCAGCAGTTCTTCTGTCAGTAC
AGGGAAGTGGTGGATGTCTTCATCCTCAAGCCATTCAGGGCGTTTGCCTTTGTTACATTTGCAGATGATCAGGTTGCACA
GTCTTTTTGTGGAGAGGGCTTGATCATTAAAGGAATCAGCATTCATATATCCAATGCTGAACCTAAGCACAATAGCAATA
GACAGAAAGAA

Alignment

ORF - retro_pabe_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.45 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRV-TEDENDEPIEIPSEDDGTVLLSTVTAQFPGACG-LRYRNPVSQCMRGVRLVEGILHAPDAGW
          MSEYIRV.TEDE.DEPIEI.S.DDGTVLLS.VTAQFPGACG.L.YRNPVSQCMRGVRLVEGILHAPDAGW
Retrocopy MSEYIRV<TEDEKDEPIEILSKDDGTVLLSMVTAQFPGACG<LCYRNPVSQCMRGVRLVEGILHAPDAGW

Parental  GNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD
          GNLVYVVNYPKDNKRKMDE.DASSAVKVKRAVQKTSDL.VLGL.WKTTEQDLKEYFSTFGEVLMVQVKKD
Retrocopy GNLVYVVNYPKDNKRKMDEIDASSAVKVKRAVQKTSDLVVLGLTWKTTEQDLKEYFSTFGEVLMVQVKKD

Parental  LKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELR
          .KTGHSK..GF..F.E.ETQVKVMSQ.HMIDGRWCDCKLPNSKQS.D.PLRS.KV.VG..TEDMT.DEL.
Retrocopy SKTGHSKRLGFICFMEDETQVKVMSQLHMIDGRWCDCKLPNSKQSPDKPLRSIKVSVGH*TEDMTADELQ

Parental  EFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLE
          .FF.QY..V.DVFI.KPFRAFAFVTFADDQ.AQS.CGE.LIIKGIS.HISNAEPKHNSNRQ.E
Retrocopy QFFCQYREVVDVFILKPFRAFAFVTFADDQVAQSFCGEGLIIKGISIHISNAEPKHNSNRQKE

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	142.48 RPM
SRP007412_cerebellum	0.00 RPM	212.80 RPM
SRP007412_heart	0.00 RPM	79.53 RPM
SRP007412_kidney	0.00 RPM	134.44 RPM
SRP007412_liver	0.00 RPM	101.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1008 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1008 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1209
Pan troglodytes	retro_ptro_828

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008 ,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,