RetrogeneDB ID: retro_acar_1

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:47882301..47882595(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000015991
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000003039
• Aliases: None
• Description: None

Sequence

>retro_acar_1
AAAAAAATGAACAAAGATGCACAAATGAGAGCAACTATTAACCAAAAGCTAATTGAAACAGGAGAACGAGAGCGCCTTAA
AGAATTACTGAGATCCAAATTAAATGAATGTGGTTGGAAAGACCAGTTGAAGGCACACTGTAAAGAGGTCATCAAGGAGA
AGGGATTAGAACATGTCACAGTTGATGATTTGGTGGCAGAAATCACTCCAAAAGGCAGAGCCTTGGTGCCTGACAGTGTA
AAGAAAGAGCTACAAAGAATAAGATCATTCCTTGCCCAGCATGTCAGCCTTTGA

Alignment

ORF - retro_acar_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNKDAQMRATINQKLIETGERERLKELLRAKLIECGWKDQLKAHCKDVIKEKGLEHVTVDDLVAEITPKG
          MNKDAQMRATINQKLIETGERERLKELLR.KL.ECGWKDQLKAHCK.VIKEKGLEHVTVDDLVAEITPKG
Retrocopy MNKDAQMRATINQKLIETGERERLKELLRSKLNECGWKDQLKAHCKEVIKEKGLEHVTVDDLVAEITPKG

Parental  RALVPDSVKKELLQRIRTFLAQHASL
          RALVPDSVKKEL.QRIR.FLAQH.SL
Retrocopy RALVPDSVKKEL-QRIRSFLAQHVSL

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	0.03 RPM	71.98 RPM
SRP009831_brain	0.19 RPM	32.05 RPM
SRP009831_dewlap	0.00 RPM	100.57 RPM
SRP009831_embryo	0.00 RPM	56.67 RPM
SRP009831_heart	0.00 RPM	16.14 RPM
SRP009831_liver	0.00 RPM	22.17 RPM
SRP009831_lung	0.15 RPM	14.15 RPM
SRP009831_ovary	0.04 RPM	92.51 RPM
SRP009831_skeletal_muscle	0.00 RPM	9.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_1 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_1 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 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003039	1 retrocopy	retro_acar_1 ,
Bos taurus	ENSBTAG00000007387	1 retrocopy	retro_btau_754,
Callithrix jacchus	ENSCJAG00000006389	4 retrocopies	retro_cjac_1206, retro_cjac_1355, retro_cjac_1436, retro_cjac_550,
Cavia porcellus	ENSCPOG00000010988	1 retrocopy	retro_cpor_927,
Dasypus novemcinctus	ENSDNOG00000007377	1 retrocopy	retro_dnov_25,
Equus caballus	ENSECAG00000023565	1 retrocopy	retro_ecab_715,
Erinaceus europaeus	ENSEEUG00000012383	3 retrocopies	retro_eeur_125, retro_eeur_220, retro_eeur_512,
Echinops telfairi	ENSETEG00000010882	2 retrocopies	retro_etel_1826, retro_etel_450,
Microcebus murinus	ENSMICG00000012948	3 retrocopies	retro_mmur_1041, retro_mmur_773, retro_mmur_793,
Myotis lucifugus	ENSMLUG00000027585	1 retrocopy	retro_mluc_357,
Macaca mulatta	ENSMMUG00000006104	2 retrocopies	retro_mmul_1094, retro_mmul_1490,
Mustela putorius furo	ENSMPUG00000005873	2 retrocopies	retro_mputfur_1128, retro_mputfur_323,
Mus musculus	ENSMUSG00000022338	3 retrocopies	retro_mmus_1055, retro_mmus_1795, retro_mmus_3511,
Nomascus leucogenys	ENSNLEG00000004284	3 retrocopies	retro_nleu_2535, retro_nleu_2584, retro_nleu_2585,
Pongo abelii	ENSPPYG00000025888	1 retrocopy	retro_pabe_750,
Rattus norvegicus	ENSRNOG00000004681	1 retrocopy	retro_rnor_2193,
Sorex araneus	ENSSARG00000009845	1 retrocopy	retro_sara_561,
Sarcophilus harrisii	ENSSHAG00000001787	4 retrocopies	retro_shar_454, retro_shar_675, retro_shar_815, retro_shar_816,
Tupaia belangeri	ENSTBEG00000000273	4 retrocopies	retro_tbel_2257, retro_tbel_324, retro_tbel_4307, retro_tbel_823,
Tarsius syrichta	ENSTSYG00000005590	1 retrocopy	retro_tsyr_673,
Tursiops truncatus	ENSTTRG00000001742	3 retrocopies	retro_ttru_46, retro_ttru_845, retro_ttru_997,