RetrogeneDB ID: retro_pabe_2915

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:147364630..147365184(+)
• Located in intron of: ENSPPYG00000017070

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDD1
• Ensembl ID: ENSPPYG00000013235
• Aliases: RHBDD1, RRP4
• Description: rhomboid domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001125444]

Sequence

>retro_pabe_2915
TTTCTGGATGAACCTGGCTTCAGAAGGTACTGTGCTGTAGGTTTTTCTAGGAGTTTTGTTTGCTTTGGAGTTTTAACAAC
CATCATTGCCTTGGAGGCTTTGTCAACATTTTGAGCTTCCTTGTCCTCAACAGATTTGCTTGTTGGGCCACACTTGTGCC
TTTTCACTTATTCTCAACCAGGGACTTCTTTCACTGGGCATCTGGCTGGGATTCATTAATGCACACTCAAGGGCCTCTGA
AGAACATCATGGAAGCATGTGCGAGCATTTTTTTCCCTCCAGTTATTGGTTATCCAGGACAGTGATATCACTTCAATTGT
TCAGGCTAGTCTGGATATCAGGATCATTATCTTTATGGCAGGCCAGGTTATTATGAAGAAGCACCCAGGAGCTATGATAT
ATACACAGCAGAACGGAGAGAAAAGGAACAGCTGGTGAGAGCATGAAGAGCCAGCCCCTGGGATCGAGAAAATACCAGGA
ATAGCTCACTGCCCTGCGGGCTTCTTCTCTCAGAAGAAATGAGACTATAATGGCTTCACAGGTTTGATAGTGAG

Alignment

ORF - retro_pabe_2915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.73 %
• Parental protein coverage: 59.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FMDEPDFKRSCAVGFSGVLFALKVL-NNHYCPGGFVNILGFPVPNRFACWVELVAIHLFSPGTSFAGHLA
          F.DEP.F.R.CAVGFS.......VL.NNH.C.GGFVNIL.F.V.NRFACW..LV..HLFS....F..H.A
Retrocopy FLDEPGFRRYCAVGFSRSFVCFGVL<NNHHCLGGFVNILSFLVLNRFACWATLVPFHLFSTRDFF--HWA

Parental  GILVGLMYTQGPLKKIMEACAGLGGFSSSVGYPGQQYYFNSSGSSGYQDYYPHGRPDHYEEAPRNYDTYT
          .....LM.TQGPLK.IMEACA....F....GYPGQ.Y.FN.SG.SGYQD.Y..GRP..YEEAPR.YD.YT
Retrocopy SGWDSLMHTQGPLKNIMEACASIF-FPPVIGYPGQ*YHFNCSG*SGYQDHYLYGRPGYYEEAPRSYDIYT

Parental  AGLSEEEQLERALQASLWDRGHTRNSPPPYGFHLSPEEEMRRQRLHRFDSQ
          A...E.EQL.RA..AS.WDR..TRNS..P.G..LS..EEMR...LHRFDS.
Retrocopy AERREKEQLVRA*RASPWDRENTRNSSLPCGLLLS--EEMRL*WLHRFDSE

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	2.99 RPM
SRP007412_cerebellum	0.00 RPM	4.62 RPM
SRP007412_heart	0.00 RPM	7.59 RPM
SRP007412_kidney	0.00 RPM	9.12 RPM
SRP007412_liver	0.03 RPM	9.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2915 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2915 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3529
Pan troglodytes	retro_ptro_2397
Gorilla gorilla	retro_ggor_2386
Callithrix jacchus	retro_cjac_2386

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012767	1 retrocopy	retro_cjac_2386,
Homo sapiens	ENSG00000144468	1 retrocopy	retro_hsap_3529,
Gorilla gorilla	ENSGGOG00000000723	1 retrocopy	retro_ggor_2386,
Pongo abelii	ENSPPYG00000013235	1 retrocopy	retro_pabe_2915 ,
Pan troglodytes	ENSPTRG00000012990	1 retrocopy	retro_ptro_2397,