RetrogeneDB ID: retro_ggal_25

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: Z:31800662..31801219(-)
• Located in intron of: ENSGALG00000015105

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8A
• Ensembl ID: ENSGALG00000008314
• Aliases: None
• Description: ADP-ribosylation factor-like protein 8A [Source:RefSeq peptide;Acc:NP_001012886]

Sequence

>retro_ggal_25
ATGCTGGCCCTTTTCAGTGAGCTGTTGGACTCATTCCAGGTGCTTCTCTGGAAGGAGAAGATGGTGCTGACCCTAGTGGG
GCTACAGTTGACAAAGACCGCCTTTGTCAATGTCATTATGTCAGGCCAGTTCAAGGAAGACACAATCCCAAAGGTGGGCT
TCAGTATGAGGAGGCCCACAAAGGGGAGGGTTACTGTAAAACTCTGGGATGTAGGTCATGACCAGCTGTACTTTCACAGC
ATGCGAGAGCCACACTGCTGTGGAGTGAGTGCCATTGTGTACGTAGTGGCTGTTGCTGCCCAGGAGAAGCTTAGGCCTTG
AAGAATGAACTTCACAACCTGCAAGACAAGCTGGAGCACCAGAGCATCCCAGCCCTAGTACTGGGGGATCAAGGGAGACC
TCTCTGGTGCCTTGGATGAGAAAGAACTCTGTTGAGAAGATGAACCTCTCTGCCATCTAGGATTGAGATTTGTTGCTACT
CTATCTCCTGCAAAGAAAAGGAAAACATCGACATCACCCTACAGTGGCTTATTCAGCACTTGGAGTTCAGGAGAAGT

Alignment

ORF - retro_ggal_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLALLSRLLDWFRSLFWKEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIW
          MLAL.S.LLD.F..L.WKE.M.LTLVGLQ...KT.FVNVI.SGQF.ED.IP.VGF.MR..TKG.VT.K.W
Retrocopy MLALFSELLDSFQVLLWKEKMVLTLVGLQLT-KTAFVNVIMSGQFKEDTIPKVGFSMRRPTKGRVTVKLW

Parental  DIG-GQPRFRSMWERYCRGVNAIVYMVDAADREKIE-ASRNELHNLLDKPQLQGIPVLVLGN-KRDLPNA
          D.G..Q..F.SM.E..C.GV.AIVY.V..A..EK...A..NELHNL.DK...Q.IP.LVLG..K.DL..A
Retrocopy DVGHDQLYFHSMREPHCCGVSAIVYVVAVAAQEKLR<ALKNELHNLQDKLEHQSIPALVLGD>KGDLSGA

Parental  LDEKQL-IEKMNLAAIQDREI-CCYSISCKEKDNIDITLQWLIQHSKSRRS
          LDEK.L..EKMNL.AI.D....C.YSISCKEK.NIDITLQWLIQH...RRS
Retrocopy LDEKEL>VEKMNLSAI*D*DL>C-YSISCKEKENIDITLQWLIQHLEFRRS

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	42.81 RPM
SRP007412_cerebellum	0.53 RPM	30.84 RPM
SRP007412_heart	0.10 RPM	14.94 RPM
SRP007412_kidney	0.06 RPM	16.98 RPM
SRP007412_liver	0.06 RPM	9.41 RPM
SRP007412_testis	0.50 RPM	15.01 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_25 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_25 has 1 orthologous retrocopies within neognath group .

Species	RetrogeneDB ID
Meleagris gallopavo	retro_mgal_18

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007757	2 retrocopies	retro_chof_1196, retro_chof_2630,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gallus gallus	ENSGALG00000008314	1 retrocopy	retro_ggal_25 ,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Microcebus murinus	ENSMICG00000000244	2 retrocopies	retro_mmur_1220, retro_mmur_1239,
Mustela putorius furo	ENSMPUG00000017035	2 retrocopies	retro_mputfur_1390, retro_mputfur_541,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343,
Tarsius syrichta	ENSTSYG00000001724	1 retrocopy	retro_tsyr_2150,
Vicugna pacos	ENSVPAG00000012114	2 retrocopies	retro_vpac_495, retro_vpac_519,