RetrogeneDB ID: retro_ecab_799

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:237564..238072(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSECAG00000000438
• Aliases: None
• Description: voltage-dependent anion channel 3 [Source:HGNC Symbol;Acc:12674]

Sequence

>retro_ecab_799
AAACACAGAAAATTAAAGGCTTCCCATAAACAGGATTGTGCCAGTCTTGGCAATAATGCTGATAGAGATTTTTCTAGAAC
AACAGTTTATGGATGAGCTCTGCTGGCCTTTGAACATTGGCTCGATGGCCATCAGAGCAGTTCTGATACAGGCAAATCCA
AACTGTCGGAGAATGTCACCCTGGGTCGCAAATCTTCAGACTTTTACATGAAGATTCATGTGAATGATGGCACTGAATTT
GGAAATTTTTTCTATAAGAAGGTTAATGAGAAAATTGAAGCTTCAGATAAATCTTGTTTGGACAGCTGGTTAGTGACAAC
ACCCAATTTTGCATGACTGCCAAATACAAACTGGATTGTGGAACTTCTGTTCTTGGTAAATTACTAATTACCAGCCTGAA
TGCACAAGGGTCTACTCAGACCCTTCAACCAAGAGTTGGATCGATCCTGGCAGCTTAAAATGATGAGAACTTCAGTCCAA
AGGTCATAAGGTTGAGCTGAGATTTGAA

Alignment

ORF - retro_ecab_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.2 %
• Parental protein coverage: 60.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSGKLKASYKRDCFSLGSNVDIDFSGPTIYGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQ
          K..KLKAS.K.DC.SLG.N.D.DFS..T.YG.A.LAFE.WL.G.Q.S.DT.KSKLS.N...LG.K..DF.
Retrocopy KHRKLKASHKQDCASLGNNADRDFSRTTVYG*ALLAFEHWLDGHQSSSDTGKSKLSEN-VTLGRKSSDFY

Parental  LHTHVNDGTEFGGSIYQKVNEKIETS-INLAWTAG-SNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGY
          ...HVNDGTEFG...Y.KVNEKIE.S.INL.WTAG.S.NT.F...AKYKLDC.TS...K....SL...G.
Retrocopy MKIHVNDGTEFGNFFYKKVNEKIEAS>INLVWTAG>SDNTQFCMTAKYKLDCGTSVLGKLLITSLNAQGS

Parental  TQTLRPGVKLTLSALIDGKNFN-AGGHKVGLGFE
          TQTL.P.V...L.A..D..NF....GHKV.L.FE
Retrocopy TQTLQPRVGSILAA*ND-ENFS<SKGHKVELRFE

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	23.43 RPM
SRP021940_cerebellum	0.00 RPM	74.11 RPM
SRP021940_embryo	0.00 RPM	79.91 RPM
SRP021940_placental_villous	0.00 RPM	34.21 RPM
SRP021940_synovial_membrane	0.00 RPM	27.64 RPM
SRP021940_testis	0.00 RPM	206.54 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_799 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_799 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2548
Pongo abelii	retro_pabe_3163

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799 ,
Equus caballus	ENSECAG00000012365	2 retrocopies	retro_ecab_831, retro_ecab_832,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,