RetrogeneDB ID: retro_pabe_1316

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:78679048..78679636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32B
• Ensembl ID: ENSPPYG00000019430
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member B [Source:HGNC Symbol;Acc:16677]

Sequence

>retro_pabe_1316
GTTCGAGAACATGTCTTGGACAACTGCAAATCAAATGACTGGAAAATTGAGAGCTTAACAGCTGAATTTGTGAACTTAGA
GTTCCTCCGTTTAATAAATGTAGGTTTGATTTCAATTTCAAATCTCCCCAAGCTGCCTAAATTGAAAAAGTTTGTACTCA
GTGAAAATAGAATCTTTGGAGGTCTGAATGTGTTTGCAGAAAAACTTCCAAATCTCACACGTTTAAACTTAAGCAGAAAA
AAACTGAAAGATATCAGCACCTTGGAACCTTTGAAAAAGTTAGAATGTCTAAAAAGCCTGGACCTCTTTAACTGTGAGGT
TATTAACCTGAATGACTACCAAGAGAGTGTCTTCAAGCTCCTGCCCCAGCTGACCTACTTGGATACCTATGACCCAGAGG
ACGAGGAAGCCCCTGACTCAGATGCCCAGGTGGATGGTGTGGATAAAGAGGAGGAGGATGAAAAAGGAGAAGGTGAGAAA
GACGAGGAGAATGAGGATGGTGAAGAAGAGTAGTTGGATGAAGACGAAGATGTAGAAGGGGATGATGACAAAGATGAAGT
CAGTAAGGAGGAAGAAGAATTTGGACTT

Alignment

ORF - retro_pabe_1316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 79.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKLKKLELSENRIFGGLDMLAEKLP
          VRE.VLDNCKSND.KIE.LTAEFVNLEFL.LINVGLIS.SNLPKLPKLKK..LSENRIFGGL...AEKLP
Retrocopy VREHVLDNCKSNDWKIESLTAEFVNLEFLRLINVGLISISNLPKLPKLKKFVLSENRIFGGLNVFAEKLP

Parental  NLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDREDQEAPDS
          NLT.LNLS..KLKDISTLEPLKKLECLKSLDLFNCEV.NLNDY.ESVFKLLPQLTYLD.YD.ED.EAPDS
Retrocopy NLTRLNLSRKKLKDISTLEPLKKLECLKSLDLFNCEVINLNDYQESVFKLLPQLTYLDTYDPEDEEAPDS

Parental  DAEVDGVDEEEEDEEGEDEEDEEDEDGEEEEFDEEDDEDEDVEGDEDDDEVSEEEEEFGL
          DA.VDGVD.EEEDE.GE.E.DEE.EDGEEE..DE..D....VEGD.D.DEVS.EEEEFGL
Retrocopy DAQVDGVDKEEEDEKGEGEKDEENEDGEEE*LDEDED----VEGDDDKDEVSKEEEEFGL

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	43.07 RPM
SRP007412_cerebellum	0.12 RPM	44.99 RPM
SRP007412_heart	0.00 RPM	45.22 RPM
SRP007412_kidney	0.00 RPM	80.98 RPM
SRP007412_liver	0.03 RPM	60.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1316 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1316 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1603
Pan troglodytes	retro_ptro_1075

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246, retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Myotis lucifugus	ENSMLUG00000004844	2 retrocopies	retro_mluc_1787, retro_mluc_1788,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316 ,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,
Tursiops truncatus	ENSTTRG00000010825	2 retrocopies	retro_ttru_1899, retro_ttru_341,