RetrogeneDB ID: retro_acar_53

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343610.1:164246..164669(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000001051
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000001719
• Aliases: None
• Description: None

Sequence

>retro_acar_53
ATGTCTGGAAGCTTCTACTTTGTAATTGTGGGTCATCATGACAATCCAGTGTTTGAAATTGAATTTCTGCCAGTTGGTAA
AGTAGAATCTAAGGATGACCATCACCATGTCAATCAATTCATAGCTTATGCTGCCCTTGACCTGGTGGATGAGAATATGT
GGCTGTCTAATAATATGTATTTGAAGACTGTGGACAAATTTAATGAATGGTTTGTCTCAGCTTTTGTTACTGCACGACGT
ATGAGATTTATAATGCTTCATGATGTAAGGCAAGAAGATGGAATCAAAAATTTCTTCAATGATGTATATGACCTGTACAT
AAAGTTTGCAATGAATCCGTTTTATGAATCCAATTCTCCAATTCGATCAACTGCATTTGACAGAAAAGTTCAGTTTCTTG
GAAAGAAGCAACTTTTAAGCTGA

Alignment

ORF - retro_acar_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVIVGHHDNPVFEMEFLPAGKVESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
          MSGSFYFVIVGHHDNPVFE.EFLP.GKVESKDDH.H.NQFIA.AALDLVDENMWLSNNMYLKTVDKFNEW
Retrocopy MSGSFYFVIVGHHDNPVFEIEFLPVGKVESKDDHHHVNQFIAYAALDLVDENMWLSNNMYLKTVDKFNEW

Parental  FVSAFVTAGHMRFIMLHDVRQEDGIKNFFNDVYDLYIKFAMNPFYESNSPIRSTAFDRKVQFLGKKHLLS
          FVSAFVTA..MRFIMLHDVRQEDGIKNFFNDVYDLYIKFAMNPFYESNSPIRSTAFDRKVQFLGKK.LLS
Retrocopy FVSAFVTARRMRFIMLHDVRQEDGIKNFFNDVYDLYIKFAMNPFYESNSPIRSTAFDRKVQFLGKKQLLS

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	3.51 RPM	29.01 RPM
SRP009831_brain	2.08 RPM	12.50 RPM
SRP009831_dewlap	3.12 RPM	22.61 RPM
SRP009831_embryo	1.04 RPM	9.66 RPM
SRP009831_heart	0.93 RPM	8.46 RPM
SRP009831_liver	1.02 RPM	12.93 RPM
SRP009831_lung	0.40 RPM	10.78 RPM
SRP009831_ovary	3.78 RPM	23.71 RPM
SRP009831_skeletal_muscle	0.76 RPM	6.08 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_53 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_53 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53 ,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,