RetrogeneDB ID: retro_pabe_3496

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:97241708..97242063(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025906
• Aliases: None
• Description: None

Sequence

>retro_pabe_3496
AATCTGCTGAGCTTGCATGTGCGGGGGTGGGGCCCTGTGTCTTCCCCCTGCACCTCCAGGCCACTGAGGTCTGCATCTGC
CCTATGGAGTTCAACCCTCACTTAGTGGCACAGTATGATACCCTAGGAGTGACCGGTGCTCCTGGAGGCAGCTGATACAT
ACCTTGCACCTGACTGGGGTGCCTAAAGGGCCGGTTGAGGGATATGAGGAGGATGAACAGTTTCTGAGGAAGATGCACCA
TGTGCTGCTGGAGGTGGATGTGTTGGAGGGCACCCTGCAGTGCCCAGAGTCTAGACGTGGGTTCTGCCTCAGCCGCAGGA
TTCCCAATATGCTGCTGAATGATGAGGAAACAGAG

Alignment

ORF - retro_pabe_3496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.5 %
• Parental protein coverage: 94.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLLSSHVRG-VGSRGFPLRLQATEVRIC-PVEFNPNFVARM-IPKVEWSAFLEAADNLRLIQVPKGPVEG
          NLLS.HVRG.VG...FPL.LQATEV.IC.P....P........P.............L.L..VPKGPVEG
Retrocopy NLLSLHVRG<VGPCVFPLHLQATEVCIC<PYGVQPSLSGTV*YPRSDRCSWRQLIHTLHLTGVPKGPVEG

Parental  YEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETE
          YEE.E.FLR.MHH.LLEV.V.EGTLQCPES.R.F..SR.IPNMLL..EETE
Retrocopy YEEDEQFLRKMHHVLLEVDVLEGTLQCPESRRGFCLSRRIPNMLLNDEETE

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	50.04 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	12.22 RPM
SRP007412_kidney	0.00 RPM	66.29 RPM
SRP007412_liver	0.03 RPM	39.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3496 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3496 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2867

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017965	3 retrocopies	retro_amel_125, retro_amel_1748, retro_amel_295,
Bos taurus	ENSBTAG00000008646	1 retrocopy	retro_btau_410,
Callithrix jacchus	ENSCJAG00000018026	1 retrocopy	retro_cjac_2995,
Equus caballus	ENSECAG00000016960	1 retrocopy	retro_ecab_103,
Homo sapiens	ENSG00000173113	4 retrocopies	retro_hsap_1853, retro_hsap_2847, retro_hsap_2974, retro_hsap_86,
Gorilla gorilla	ENSGGOG00000001334	3 retrocopies	retro_ggor_1669, retro_ggor_2157, retro_ggor_2867,
Macaca mulatta	ENSMMUG00000019647	2 retrocopies	retro_mmul_1267, retro_mmul_2181,
Nomascus leucogenys	ENSNLEG00000004991	4 retrocopies	retro_nleu_1599, retro_nleu_2137, retro_nleu_2169, retro_nleu_556,
Pongo abelii	ENSPPYG00000025906	5 retrocopies	retro_pabe_1510, retro_pabe_2357, retro_pabe_3062, retro_pabe_3332, retro_pabe_3496 ,
Pteropus vampyrus	ENSPVAG00000017134	1 retrocopy	retro_pvam_853,
Ictidomys tridecemlineatus	ENSSTOG00000019857	1 retrocopy	retro_itri_208,