RetrogeneDB ID: retro_pabe_2301

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:36511165..36511514(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSPPYG00000025898
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_pabe_2301
GGCGGCGGAGGGGGCGCAGGGGCCTGGCTGGGCGAAGGCGGGACCGCGAGCGCGGAGGCTGCGGGCCCTGCAGGGGCCAC
CACCAAGGCTGTGAAGGACGAAGGTGAATGGAAAGGCTTGGAGTAAAAAGAGGTTGATTACAGAGGCCTCGGGGTTCAGG
CAATGCAAATAAGTGAAAAGGAAGAAGATATTGAAGAGACAAGATCCAGGTGATAACTGGGAAGAAGGTGGAGGTGGTGG
TGATACAGAAAAATCTTCAGGTCCCTGGAATAAAACAGCTCCGGTACAAGCACCTCTTGCTCCAGTAATTGTTACAGAAA
CCCCAGAACTGGCAATGACTAGTGGTGTG

Alignment

ORF - retro_pabe_2301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.85 %
• Parental protein coverage: 55.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGAGAGTRPGDGGTASAGAAGPGAATKAVTKHEDEWKEIKQKEVDYSGLRVQAMQISSEKEEDDNE-KR
          GGG.GAG...G.GGTASA.AAGP.....A.TK......E.K..E......R....Q.....E......KR
Retrocopy GGGGGAGAWLGEGGTASAEAAGPAG---ATTKAVKDEGEWKGLE*KEVDYRGLGVQAMQISEKEEDI>KR

Parental  QDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPCSILVTETPEPAMTSGV
          QDPGDNWEEGGGGG...EKSSGPWNKTAPVQAP.....VTETPE.AMTSGV
Retrocopy QDPGDNWEEGGGGGD-TEKSSGPWNKTAPVQAPLAPVIVTETPELAMTSGV

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	2.49 RPM	12.39 RPM
SRP007412_cerebellum	0.61 RPM	6.81 RPM
SRP007412_heart	2.32 RPM	16.05 RPM
SRP007412_kidney	2.25 RPM	14.58 RPM
SRP007412_liver	1.96 RPM	13.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2301 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301 ,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,