RetrogeneDB ID: retro_ggal_13

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 1:180895327..180895753(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5B
• Ensembl ID: ENSGALG00000000660
• Aliases: CYB5B, CYB5-M
• Description: outer mitochondrial membrane cytochrome b5 [Source:RefSeq peptide;Acc:NP_001025752]

Sequence

>retro_ggal_13
GAGACCAGGAAGTGAACAGAAGATGGGAGCTGCGCAGCAAAGGCAAAGGAGTCTGGGCCCGTGTTCATGCTGGAGGAAGT
GGGGAAGCGGAACTCCAAACACAAGGCCAGGGTGCTCATCCATGGGTGTGTGTACAATATCACCTGCTTCCTAGAGGAGC
ATCCAGGTGGAGAAGAGGTTTTGCTTGAACAAGTTGGCAGAGATGCCACAGAGAGCTTAGATGATGTTGATCATTCCACA
GATACCAGGGAAATGCTCAAGCATTACTACATAGGGGACATCCACCCAGGTGATCGTAAAAACAAGGATGAAAATAGGTC
ATCCTCAGGATAAACAAGGTTCTGGTCAACATGCCTAATCTACATCTTTTGTGCCCTAGTCATAAGTTTATTGTGTCGCT
ATTATACGTTGGATGGGAGATCATCT

Alignment

ORF - retro_ggal_13 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.21 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESGQRTEAGGCAEEP--AGPVFTLEEVGRRNSNREAWLVIHGRVYDVTRFLEEHPGGEEVLLEQAGRDAT
          E....TE.G.CA......GPVF.LEEVG.RNS...A...IHG.VY..T.FLEEHPGGEEVLLEQ.GRDAT
Retrocopy ETRK*TEDGSCAAKAKESGPVFMLEEVGKRNSKHKARVLIHGCVYNITCFLEEHPGGEEVLLEQVGRDAT

Parental  ESFEDVGHSTDAREMLKQYYIGEIHPDDRKKGGSKDQNRTSSGQASFWTTWLIPIFGALVIGLMYRYYIL
          ES..DV.HSTD.REMLK.YYIG.IHP.DRK....KD.NR.SSG...FW.T.LI.IF.ALVI.L..RYY.L
Retrocopy ESLDDVDHSTDTREMLKHYYIGDIHPGDRK---NKDENRSSSG*TRFWSTCLIYIFCALVISLLCRYYTL

Parental  DGRSS
          DGRSS
Retrocopy DGRSS

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	0.06 RPM	40.93 RPM
SRP007412_cerebellum	0.00 RPM	33.65 RPM
SRP007412_heart	0.00 RPM	32.14 RPM
SRP007412_kidney	0.00 RPM	54.40 RPM
SRP007412_liver	0.00 RPM	36.96 RPM
SRP007412_testis	0.00 RPM	38.03 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_13 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_13 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117,
Dasypus novemcinctus	ENSDNOG00000008313	9 retrocopies	retro_dnov_1424, retro_dnov_2077, retro_dnov_2123, retro_dnov_2310, retro_dnov_2684, retro_dnov_2685, retro_dnov_706, retro_dnov_716, retro_dnov_728,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Homo sapiens	ENSG00000103018	1 retrocopy	retro_hsap_1493,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13 ,
Gorilla gorilla	ENSGGOG00000015031	1 retrocopy	retro_ggor_1146,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289,
Nomascus leucogenys	ENSNLEG00000005515	1 retrocopy	retro_nleu_1715,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pongo abelii	ENSPPYG00000007506	1 retrocopy	retro_pabe_1243,
Pan troglodytes	ENSPTRG00000008282	1 retrocopy	retro_ptro_1012,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296,
Tarsius syrichta	ENSTSYG00000014292	1 retrocopy	retro_tsyr_2171,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,