RetrogeneDB ID: retro_acar_189

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343414.1:236448..236685(+)
• Located in intron of: ENSACAG00000003580

Retrocopy information

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

Parental gene information

• Parental gene symbol: SS18L2
• Ensembl ID: ENSACAG00000000989
• Aliases: None
• Description: None

Sequence

>retro_acar_189
ATGTTGGTGGTCTTTCTGCCCGAGCGGGTGTGGGGCAAGGTGGAGATGAACCAGGAGATGCTGCAGAGGCTGATGGACGA
AAATGACCAGCTGATCCGCTTCATTGTGGAGTATCAGAACAAAGGGAGGGCCGTCAAATATATGCAGCTCCAGCACACCC
TTTGTCGGAACCTCATTTATTTGGCAATGATCGCAGATGCTCCTGCTTCATCAAACACCAAAAAGGCTGCAGCAGAC

Alignment

ORF - retro_acar_189 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVVFLPERVRGKAEVNQETLRRLMDENDQLIRCIVEYQNKGRAAECMQLQHTLHRNLIYLATIADASAS
          M.VVFLPERV.GK.E.NQE.L.RLMDENDQLIR.IVEYQNKGRA...MQLQHTL.RNLIYLA.IADA.AS
Retrocopy MLVVFLPERVWGKVEMNQEMLQRLMDENDQLIRFIVEYQNKGRAVKYMQLQHTLCRNLIYLAMIADAPAS

Parental  SNAEKAAAE
          SN..KAAA.
Retrocopy SNTKKAAAD

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
SRP009831_adrenal	0.16 RPM	37.75 RPM
SRP009831_brain	0.14 RPM	17.47 RPM
SRP009831_dewlap	0.00 RPM	55.39 RPM
SRP009831_embryo	0.03 RPM	20.27 RPM
SRP009831_heart	0.10 RPM	18.83 RPM
SRP009831_liver	0.00 RPM	29.69 RPM
SRP009831_lung	0.55 RPM	22.21 RPM
SRP009831_ovary	0.00 RPM	54.28 RPM
SRP009831_skeletal_muscle	0.00 RPM	14.13 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_189 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_189 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189 ,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Erinaceus europaeus	ENSEEUG00000014065	1 retrocopy	retro_eeur_634,
Echinops telfairi	ENSETEG00000007192	2 retrocopies	retro_etel_1749, retro_etel_2074,
Homo sapiens	ENSG00000008324	1 retrocopy	retro_hsap_557,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Macaca mulatta	ENSMMUG00000031677	1 retrocopy	retro_mmul_2392,
Mus musculus	ENSMUSG00000032526	3 retrocopies	retro_mmus_1247, retro_mmus_1827, retro_mmus_3284,
Nomascus leucogenys	ENSNLEG00000005848	1 retrocopy	retro_nleu_2639,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Pongo abelii	ENSPPYG00000013979	2 retrocopies	retro_pabe_513, retro_pabe_651,
Sorex araneus	ENSSARG00000014056	1 retrocopy	retro_sara_465,
Tarsius syrichta	ENSTSYG00000007658	1 retrocopy	retro_tsyr_1687,