RetrogeneDB ID: retro_pabe_3003

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:129970843..129971172(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSPPYG00000000183
• Aliases: None
• Description: protein cornichon homolog 4 [Source:RefSeq peptide;Acc:NP_001125902]

Sequence

>retro_pabe_3003
GAGGACATGGTCTTTGTCTTCTTTCTCCTCAGTTGCAGGCTCATTTTTCTCTCAGTGTTCATAATTACATTGTCTGATTT
AGAGAGTGATTACATTAATGCTAGATCATGTTGCTCAAAATTAAACAAGTGGGTAATTCCAAGATTGATTGGCCGTACTA
TTGTCACTGTATTATGCGCATTTTGTTGCACTGGTTCATCTTCCTTCTCAACTTACCTCTTGCCACTTGGAATACATATT
GATTCATTATGGTGCCAAGCAGTAACATAGGAGTGTTTGATCCAACAGAAATACACAATCAAGGACAGCAAAAGTAACAC
ATGAAAGAC

Alignment

ORF - retro_pabe_3003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAVVFVFSLLDCCALIFLSVYFIITLSDLECDYINARSCCSKLNKWVIPELIGHTIVTVL-LLISLHWFI
          E..VFVF.LL.C..LIFLSV.FIITLSDLE.DYINARSCCSKLNKWVIP.LIG.TIVTVL...I.LHWFI
Retrocopy EDMVFVFFLLSC-RLIFLSV-FIITLSDLESDYINARSCCSKLNKWVIPRLIGRTIVTVL<MRILLHWFI

Parental  FLLNLPVATWNIYRYIMVPSGNMGVFDPTEIHNRGQLKSHMKE
          FLLNLP.ATWN.Y..IMVPS.N.GVFDPTEIHN.GQ.K.HMK.
Retrocopy FLLNLPLATWNTY*FIMVPSSNIGVFDPTEIHNQGQQK*HMKD

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	18.19 RPM
SRP007412_cerebellum	0.00 RPM	22.01 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.03 RPM	21.11 RPM
SRP007412_liver	0.00 RPM	16.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3003 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3003 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3656
Pan troglodytes	retro_ptro_2481
Macaca mulatta	retro_mmul_1796

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003 ,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,