RetrogeneDB ID: retro_ggal_15

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 2:76684717..76685008(+)
• Located in intron of: ENSGALG00000012997

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf45
• Ensembl ID: ENSGALG00000012694
• Aliases: C12ORF45, C1H12orf45
• Description: chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]

Sequence

>retro_ggal_15
CTGGTTGGTATCTTTAAAATTACTGGATACTTAATCTCTCAGACTATAATGTCAACCAGTTACGGAGGGCTGGAAGAAAC
ATTACTGATTAGTTCAAAGCCTAGCAGCAAGAAGGCTACAACTTTACAGACAGTTAGGATGCCAAGGAGTAATGTTTTGG
ACAGAGTACAGAGCTTTTTACCGCAGATGGCGCATGCAAATGATGAGCTAAGAAGAAAAATGTTAACAGAACCAGCTCAT
CAGTTTGATATTGAAAATCTCAGCAGTGCCACAGAAAAAGTGATAGAAATG

Alignment

ORF - retro_ggal_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGVGQAAGPAASRELLAAGRRGGLEETLLISPKPSSKKATTLQTVRMPRSNVLDRVQSFLPQMAHANDE
          ..G.....G...S.........GGLEETLLIS.KPSSKKATTLQTVRMPRSNVLDRVQSFLPQMAHANDE
Retrocopy LVGIFKITGYLISQTIMSTSY-GGLEETLLISSKPSSKKATTLQTVRMPRSNVLDRVQSFLPQMAHANDE

Parental  LRRKMVTAPAHQFDIENLSSATEKVIEM
          LRRKM.T.PAHQFDIENLSSATEKVIEM
Retrocopy LRRKMLTEPAHQFDIENLSSATEKVIEM

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	2.50 RPM
SRP007412_cerebellum	0.00 RPM	1.23 RPM
SRP007412_heart	0.00 RPM	0.64 RPM
SRP007412_kidney	0.00 RPM	1.24 RPM
SRP007412_liver	0.00 RPM	1.45 RPM
SRP007412_testis	0.03 RPM	1.91 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_15 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_15 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15 ,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105, retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,