RetrogeneDB ID: retro_ggal_14

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 1:618427..618958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSGALG00000013382
• Aliases: None
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_ggal_14
GAGAGGCGGGAGAGACGGCGGCGGGAGCTGCGGGCGTTGGCGCTGGGGCAGGGAGACTTCCAGCTGGTGGATCACCGCGG
GCGGCCCCGCTGCAAGGCCGACTTCCGGGGGCAGTGGGTGCTGCTTTACTTCGGCTTCACGCATTGCCCCGACGTCTGCC
CCGACGAGCTGGAGAAACTGAGCCGGGCGGTGGAGCTGTTGGACCGCGACGCGGCTCTGCCCCGGGTGCAGCCCCTCTTC
ATCACCGTGGACCCCGAGAGGGACGACGTGGCGGCGGTGGAGCGATACGTGCGGGATTTCCACCCGCGGCTGCTGGGGCT
GACGGGGAGCCCTGAGCAGGTGAGGGCGGTGAGCAGCGCCTACCGCGTCTACGCCAGCGCCGGGCCCAAGGATGAGGACG
GCGATTACATCGTGGACCACACCATCATCATTTACCTGCTGGGCCCCGACGGGCTCTTCTTGGACTACTACAACCGCAGC
AAGACGGCTGATAAGATCGCTGAGAGCGTGCGGCAACACATGGAGAGCTAC

Alignment

ORF - retro_ggal_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.8 %
• Parental protein coverage: 90.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELEKERNRGIGKPLLG-GPFSLVSHEGQPKTNKDYLGQWVLIYFGFTHCPDICPEELDKMIEVVNEIDRI
          E....R.R......LG.G.F.LV.H.G.P....D..GQWVL.YFGFTHCPD.CP.EL.K....V...DR.
Retrocopy ERRERRRRELRALALGQGDFQLVDHRGRPRCKADFRGQWVLLYFGFTHCPDVCPDELEKLSRAVELLDRD

Parental  PSLPDLTPLFITIDPERDSEEAIARYVKEFSPKLVGLTGTRAQIDQVAKAFRVYYSEGPKDEDNDYIVDH
          ..LP...PLFIT.DPERD...A..RYV..F.P.L.GLTG...Q...V..A.RVY.S.GPKDED.DYIVDH
Retrocopy AALPRVQPLFITVDPERDDVAAVERYVRDFHPRLLGLTGSPEQVRAVSSAYRVYASAGPKDEDGDYIVDH

Parental  TIIMYLLGPDGDFVDYYGQNKKSAEISASIAAHMRKY
          TII.YLLGPDG.F.DYY...K....I..S...HM..Y
Retrocopy TIIIYLLGPDGLFLDYYNRSKTADKIAESVRQHMESY

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	4.61 RPM	17.02 RPM
SRP007412_cerebellum	2.72 RPM	13.28 RPM
SRP007412_heart	3.25 RPM	16.66 RPM
SRP007412_kidney	9.73 RPM	48.76 RPM
SRP007412_liver	6.97 RPM	24.09 RPM
SRP007412_testis	3.46 RPM	10.79 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_14 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_14 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14 ,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,