RetrogeneDB ID: retro_pabe_2112

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:44507900..44508427(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSPPYG00000017714
• Aliases: None
• Description: Chromobox protein homolog 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6X7]

Sequence

>retro_pabe_2112
AAAACGACCTCCAATAAAATTACATTGCAAAAAATGGGAAAGTAACAGAATGGGAAGTGTAAAAAAGTCAAAGAGGCAGA
GACTGAAGAATTTGTGGTGGAAATAGCAAATGGAAGCTGGAGTATTTCCCGAAGTCAAAGGGATTTACAAATGCTGACAG
TACTTAGGAACCGGAAGACTACTTAGACTGTCTAGAGTTAATTGAAACATTTCTTAATTCTCAAAAAGCTGGCAAAGAAA
AAGATGATACAAAAAGGAAATGTTTATGTGACAGTGAATCTGATGATAGCAAATCAAAGAAAAGAGATGCTGCTGACAAA
CCAAGAGGCTTCGCCAGAGGTCATGATCCAGAAAGAAAAATTGCCACAGAGAGAAGTGGGGAATGGATATTTCTCCTGGA
ATGGGAACATTCAGATGAGGCAGACTTGCTGCAGGCAAAAGAGGCAAACCTGAGGAGTCATCAAATTGTAATTGCTTCTT
ATGAAGAGCGATTGCCTTGACATTCTTGAGGAGAAGATGAAGCTCAA

Alignment

ORF - retro_pabe_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 97.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNG-KVEYFLKWKGFTDADNTWEPEENLDCPELI
          KTT..K......GK..........E...E........NG.K.EYF.K.KGFT.AD.T.EPE..LDC.ELI
Retrocopy KTTSNKITLQKMGK*QNGKCKKVKEAETEEFVVE-IANG<KLEYFPKSKGFTNADST*EPEDYLDCLELI

Parental  EAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWK
          E.FLNSQKAGKEKD.TKRK.L.DSESDDSKS.KKRDAADKPRGFARG.DPER.I.AT..SGE..FL..W.
Retrocopy ETFLNSQKAGKEKDDTKRKCLCDSESDDSKS-KKRDAADKPRGFARGHDPERKI-ATERSGEWIFLLEWE

Parental  DSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          .SDEADL..AKEAN....QIVIA.YEERL..HS..EDEAQ
Retrocopy HSDEADLLQAKEANLRSHQIVIASYEERLP*HS*GEDEAQ

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	35.05 RPM
SRP007412_cerebellum	0.12 RPM	54.60 RPM
SRP007412_heart	0.00 RPM	29.92 RPM
SRP007412_kidney	0.00 RPM	36.53 RPM
SRP007412_liver	0.00 RPM	25.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2112 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2112 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2332
Pan troglodytes	retro_ptro_1706

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Dipodomys ordii	ENSDORG00000005487	11 retrocopies	retro_dord_309, retro_dord_405, retro_dord_437, retro_dord_440, retro_dord_456, retro_dord_502, retro_dord_629, retro_dord_630, retro_dord_655, retro_dord_700, retro_dord_780,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Myotis lucifugus	ENSMLUG00000007591	2 retrocopies	retro_mluc_2486, retro_mluc_813,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Pongo abelii	ENSPPYG00000017714	10 retrocopies	retro_pabe_2112 , retro_pabe_2243, retro_pabe_2724, retro_pabe_2770, retro_pabe_2997, retro_pabe_3608, retro_pabe_758, retro_pabe_786, retro_pabe_892, retro_pabe_951,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,