RetrogeneDB ID: retro_pabe_343

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:202191841..202192144(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8B
• Ensembl ID: ENSPPYG00000013694
• Aliases: None
• Description: ADP-ribosylation factor-like protein 8B [Source:RefSeq peptide;Acc:NP_001126561]

Sequence

>retro_pabe_343
CAAGGTAACGTCACAATAAAGATCTAGGACATAGGAGGACAAGCCGGATTTCGAAGCATGTGGGAGCGGTATTGCAGAGG
AGTCAGTGCTATTGTTTACATGATAGATGCTGCAGATCGTGAAAAGATAGAAGCTTCCCGAAATGAGCTACATAATCTTC
TAGAGAAACCACAGTTGCAAGGAATTCCAGTGCTAAGTGCTTGGAAACAAGGGAGATCTTCTAATGCCTTGGATGAGAAA
CAGCTAATTGAAAAAATGAGCCTGTCTGCTATTCAGGATAGAGAAGTTTGCCGCTATTCGATT

Alignment

ORF - retro_pabe_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.38 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVL-VLGN
          .GNVTIKI.DIGGQ..FRSMWERYCRGV.AIVYMIDAADREKIEASRNELHNLL.KPQLQGIPVL.VLGN
Retrocopy QGNVTIKI*DIGGQAGFRSMWERYCRGVSAIVYMIDAADREKIEASRNELHNLLEKPQLQGIPVL>VLGN

Parental  KRDL-PNALDEKQLIEKMNLSAIQDREICCYSI
          K.DL..NALDEKQLIEKM.LSAIQDRE.C.YSI
Retrocopy KGDL<SNALDEKQLIEKMSLSAIQDREVCRYSI

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	0.11 RPM	90.01 RPM
SRP007412_cerebellum	0.12 RPM	90.23 RPM
SRP007412_heart	0.03 RPM	31.76 RPM
SRP007412_kidney	0.00 RPM	36.13 RPM
SRP007412_liver	0.00 RPM	25.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_343 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_343 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007757	2 retrocopies	retro_chof_1196, retro_chof_2630,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Gallus gallus	ENSGALG00000008314	1 retrocopy	retro_ggal_25,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Microcebus murinus	ENSMICG00000000244	2 retrocopies	retro_mmur_1220, retro_mmur_1239,
Mustela putorius furo	ENSMPUG00000017035	2 retrocopies	retro_mputfur_1390, retro_mputfur_541,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343 ,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Tarsius syrichta	ENSTSYG00000001724	1 retrocopy	retro_tsyr_2150,
Vicugna pacos	ENSVPAG00000012114	2 retrocopies	retro_vpac_495, retro_vpac_519,