RetrogeneDB ID: retro_ggal_11

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 1:122099711..122100226(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSGALG00000003755
• Aliases: None
• Description: None

Sequence

>retro_ggal_11
AGGAAGAGTGAAAAGTTGAAGGCCTCCTATAAAGGAGAATATGTAAATCTAGGCTGCAATATAGACTTTGATCTCTCTGG
ACCAGCCATTTATGCCTGGGCAGTGCTGGGTTATGAAGGTTGGCCGGCTGGATATCAGATGACTTTTATACAGCCAAATC
TAAGCTTTCACAAAACAACTTTGCCTTGGGATATAAGGCAGGAGACTTTCAGCTGCACACTAATGTGAATGGTGGCACAG
AGTTTAGTGGGTCTATTTATCAGAAGGTTAATAATAAGGTTGAGACGTCAGTTAATCTTGCAAGGACTTCTGGCAGTAAC
AACACGCAGTTTGGTATTGCTGCTAAGTACCAACTGGACGAGAAGACTTCCACTGTGAGTAATGCCAGCCTGACAGGAAT
TGGTTACACTCTTGCTCTTTGACCTGGTGTAAGGCTGACCCTCTCAGGTTTGACTGATGGCAAGAATTTCAGTGCTGGAA
GTCACAAAGTTGGGCTAGGATTTGAGCTGGAAGCT

Alignment

ORF - retro_ggal_11 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKSGKLKTSYRRDYVNLGCNIDIDLSGPTIYGWAVLGYEGWLAGYQMAFD-TAKSKLSQNNFALGYKAGD
          .KS.KLK.SY...YVNLGCNID.DLSGP.IY.WAVLGYEGW.AGYQM.F..TAKSKLSQNNFALGYKAGD
Retrocopy RKSEKLKASYKGEYVNLGCNIDFDLSGPAIYAWAVLGYEGWPAGYQMTFI<TAKSKLSQNNFALGYKAGD

Parental  FQLHTNVNDGTEFGGSIYQKVNNKVETSVNLAWTAGSNNTRFGIAAKYQLDEKTSIGAKVNNASLIGIGY
          FQLHTNVN.GTEF.GSIYQKVNNKVETSVNLA.T.GSNNT.FGIAAKYQLDEKTS....V.NASL.GIGY
Retrocopy FQLHTNVNGGTEFSGSIYQKVNNKVETSVNLARTSGSNNTQFGIAAKYQLDEKTS---TVSNASLTGIGY

Parental  TLALRPGVKLTLSGLIDGKNFSAGGHKVGLGFELEA
          TLAL.PGV.LTLSGL.DGKNFSAG.HKVGLGFELEA
Retrocopy TLAL*PGVRLTLSGLTDGKNFSAGSHKVGLGFELEA

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	0.00 RPM	72.23 RPM
SRP007412_cerebellum	0.04 RPM	66.38 RPM
SRP007412_heart	0.10 RPM	53.23 RPM
SRP007412_kidney	0.00 RPM	28.44 RPM
SRP007412_liver	0.00 RPM	13.64 RPM
SRP007412_testis	0.09 RPM	29.61 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_11 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_11 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 56 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,
Echinops telfairi	ENSETEG00000002652	2 retrocopies	retro_etel_1456, retro_etel_1487,
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,
Tursiops truncatus	ENSTTRG00000009681	3 retrocopies	retro_ttru_1201, retro_ttru_1254, retro_ttru_634,