RetrogeneDB ID: retro_ecab_235

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:26985822..26986260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSECAG00000000682
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_ecab_235
GCCATGAGTTTATCGCAGTGGGCTTTGGTCACTGTGGCAGCCAGAGTGGCCACCATCTTGGGACTCAACTTAGATTCAGG
GACGTCTTCACCCGCAGCCTTCTGAAGACTGTAGCTCCTGTGTGACACAGTGGAGGCCACAGGAAAGGACTGTTTATCCT
ATCTTCTGGATTCTGTGATAGTGTTTTTTGGAATTTAGTGAAACTCTATATTTTGTTGACTGGGATTGCAGTGGCATTGG
CATAACTCTGGTGAATGTATTCATTGGTGAAGCTGAGTTAGCAGAAATTCCAAAAGGCTATGTTCCAGGACACTGGGAAT
ATTTCAACCATCCTCTATCAAGATGAACTTCCTGTACTTTCTTTGATGTTCCTGGGAAGAATCATGAAAAAACAATGCCT
ATCCTTTAAATGAAGCCAAAAAGGCTGAATTACAGTTA

Alignment

ORF - retro_ecab_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.25 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AMSLLQRASVAAA-SLCGRRLGPRHAFGGFLTRGFPKTVAPVRHSGGHGKRLFIIKPSGFYDRRFLNLMR
          AMSL.Q.A.V..A.S..G..LG....F....TR...KTVAPV.HSGGH.K.LFI...SGF.D..F.NL..
Retrocopy AMSLSQWALVTVA<SQSGHHLGTQLRFRDVFTRSLLKTVAPV*HSGGHRKGLFILS-SGFCDSVFWNLVK

Parental  FYILLTGIPVA-IGITLINVFIGEAELAEIPEGYIPEHWEYFKHPISRWIARTFFDSPEKNYEKTLAILQ
          .YILLTGI.VA.IGITL.NVFIGEAELAEIP.GY.P.HWEYF.HP.SR....TFFD.P.KN.EKT..IL.
Retrocopy LYILLTGIAVA<IGITLVNVFIGEAELAEIPKGYVPGHWEYFNHPLSR*TSCTFFDVPGKNHEKTMPIL*

Parental  I-EAEKADLRL
          ..EA.KA.L.L
Retrocopy M<EAKKAELQL

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
SRP021940_articular_cartilage	0.00 RPM	8.21 RPM
SRP021940_cerebellum	0.05 RPM	40.51 RPM
SRP021940_embryo	0.08 RPM	21.61 RPM
SRP021940_placental_villous	0.00 RPM	28.96 RPM
SRP021940_synovial_membrane	0.00 RPM	12.38 RPM
SRP021940_testis	0.00 RPM	26.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_235 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002684	1 retrocopy	retro_chof_1511,
Equus caballus	ENSECAG00000000682	1 retrocopy	retro_ecab_235 ,
Echinops telfairi	ENSETEG00000019363	1 retrocopy	retro_etel_1110,
Homo sapiens	ENSG00000136521	2 retrocopies	retro_hsap_3127, retro_hsap_4879,
Macropus eugenii	ENSMEUG00000014166	1 retrocopy	retro_meug_1852,
Myotis lucifugus	ENSMLUG00000000999	1 retrocopy	retro_mluc_2181,
Macaca mulatta	ENSMMUG00000009746	1 retrocopy	retro_mmul_2619,
Monodelphis domestica	ENSMODG00000021300	1 retrocopy	retro_mdom_1105,
Nomascus leucogenys	ENSNLEG00000005842	2 retrocopies	retro_nleu_2247, retro_nleu_2558,
Pongo abelii	ENSPPYG00000014493	2 retrocopies	retro_pabe_3018, retro_pabe_3796,
Pan troglodytes	ENSPTRG00000015649	1 retrocopy	retro_ptro_3252,
Pteropus vampyrus	ENSPVAG00000004286	1 retrocopy	retro_pvam_81,
Sorex araneus	ENSSARG00000006918	1 retrocopy	retro_sara_200,
Sus scrofa	ENSSSCG00000011764	1 retrocopy	retro_sscr_193,
Ictidomys tridecemlineatus	ENSSTOG00000010557	1 retrocopy	retro_itri_1810,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,