RetrogeneDB ID: retro_pabe_810

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:5733068..5733356(+)
• Located in intron of: ENSPPYG00000004179

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLRB1
• Ensembl ID: ENSPPYG00000010937
• Aliases: None
• Description: dynein, light chain, roadblock-type 1 [Source:HGNC Symbol;Acc:15468]

Sequence

>retro_pabe_810
ATGTCAGAGGTGGAGGAGACACTGAAGTGACTTCAGAGCCAGAGGGGACTGCAGAATATCACCATGGTGAACAAAGATGG
CATTCCCATCAAGAGCACCATGGTCAACCTCAGCACCACACAGTGCGCCAGCCTCATGCACAGCTTCATCCTGAAGGCAC
GGAGCACCGTGCATGAAAATGACCCCCAGAATGATCTCACCTTCCTTCAAATTTGCTCCAAGAAAAATGAAATTATGGTT
GCACCAGATAAAGACTATTTCCTGATTGTGATTCAGAATCCAAATGAA

Alignment

ORF - retro_pabe_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLR
          M.EVEETLK.LQSQ.G.Q.I..VN..GIPIKSTM.N..TTQ.ASLMHSFILKARSTV...DPQNDLTFL.
Retrocopy MSEVEETLK*LQSQRGLQNITMVNKDGIPIKSTMVNLSTTQCASLMHSFILKARSTVHENDPQNDLTFLQ

Parental  IRSKKNEIMVAPDKDYFLIVIQNPTE
          I.SKKNEIMVAPDKDYFLIVIQNP.E
Retrocopy ICSKKNEIMVAPDKDYFLIVIQNPNE

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	331.30 RPM
SRP007412_cerebellum	0.00 RPM	120.02 RPM
SRP007412_heart	0.03 RPM	45.64 RPM
SRP007412_kidney	0.00 RPM	130.76 RPM
SRP007412_liver	0.00 RPM	51.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_810 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_810 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_948
Gorilla gorilla	retro_ggor_764
Macaca mulatta	retro_mmul_779

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009179	1 retrocopy	retro_amel_1111,
Canis familiaris	ENSCAFG00000007547	6 retrocopies	retro_cfam_1161, retro_cfam_1294, retro_cfam_1577, retro_cfam_1601, retro_cfam_1782, retro_cfam_930,
Callithrix jacchus	ENSCJAG00000018199	10 retrocopies	retro_cjac_1010, retro_cjac_1172, retro_cjac_1274, retro_cjac_1539, retro_cjac_2071, retro_cjac_2902, retro_cjac_3185, retro_cjac_3215, retro_cjac_3260, retro_cjac_882,
Equus caballus	ENSECAG00000008404	2 retrocopies	retro_ecab_102, retro_ecab_553,
Echinops telfairi	ENSETEG00000018637	2 retrocopies	retro_etel_218, retro_etel_699,
Felis catus	ENSFCAG00000002304	1 retrocopy	retro_fcat_1228,
Homo sapiens	ENSG00000125971	2 retrocopies	retro_hsap_1946, retro_hsap_948,
Gorilla gorilla	ENSGGOG00000023900	1 retrocopy	retro_ggor_764,
Loxodonta africana	ENSLAFG00000029820	2 retrocopies	retro_lafr_722, retro_lafr_852,
Microcebus murinus	ENSMICG00000003253	1 retrocopy	retro_mmur_263,
Myotis lucifugus	ENSMLUG00000004820	3 retrocopies	retro_mluc_1200, retro_mluc_1763, retro_mluc_443,
Macaca mulatta	ENSMMUG00000031253	1 retrocopy	retro_mmul_779,
Nomascus leucogenys	ENSNLEG00000010082	2 retrocopies	retro_nleu_1478, retro_nleu_2456,
Oryctolagus cuniculus	ENSOCUG00000021027	2 retrocopies	retro_ocun_351, retro_ocun_745,
Otolemur garnettii	ENSOGAG00000016802	2 retrocopies	retro_ogar_7, retro_ogar_983,
Ochotona princeps	ENSOPRG00000004714	1 retrocopy	retro_opri_888,
Pongo abelii	ENSPPYG00000010937	1 retrocopy	retro_pabe_810 ,
Pan troglodytes	ENSPTRG00000013416	1 retrocopy	retro_ptro_655,
Rattus norvegicus	ENSRNOG00000025715	1 retrocopy	retro_rnor_1883,
Ictidomys tridecemlineatus	ENSSTOG00000014820	1 retrocopy	retro_itri_1244,