RetrogeneDB ID: retro_acar_196

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343577.1:21043..21369(-)
• Located in intron of: ENSACAG00000006061

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000026874
• Aliases: None
• Description: None

Sequence

>retro_acar_196
GAGGGTAAGGGAGATGGGAAATTCTGGAAATGCGGAAAACATAACTGAGATTTTATACACATGTGGTGGGGATGTAGGAA
AATAAAAAGGCTTTGGCAGGAAATCAACAAAGAAATGGAGAAAATACTCCAAATTAAATTTGATTTAAAACCAGAATACT
TCCTTCTAGGTATTGTAGATTTTCAGATTGATTCCAATACAGAAAAACTCTTCATATATATATGGTAACAGCTGCCAGGA
TATGTATAGCCAAAGTATGGAAAATGCAAGAAATCCCCACAATAGAAAAATGGATGCTGAAACTAATAGACATTAAAAAT
ATGGAT

Alignment

ORF - retro_acar_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 59.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGEGDGKCWKCQKHNGDFMHMWWGCRKIKKFWQEINREMEKILQIKFNTKPEYFLLGMVDFQMD-FNREK
          .G.GDGK.WKC.KHN.DF.HMWWGCRKIK..WQEIN.EMEKILQIKF..KPEYFLLG.VDFQ.D.F...K
Retrocopy EGKGDGKFWKCGKHN*DFIHMWWGCRKIKRLWQEINKEMEKILQIKFDLKPEYFLLGIVDFQID<FQYRK

Parental  LFIYLYFLINFIICIAKLWKTQETPTLETWILKLIDIKNMD
          .....Y......ICIAK.WK.QE.PT.E.W.LKLIDIKNMD
Retrocopy T-LHIYMVTAARICIAKVWKMQEIPTIEKWMLKLIDIKNMD

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	0.07 RPM	0.07 RPM
SRP009831_brain	0.09 RPM	0.00 RPM
SRP009831_dewlap	0.00 RPM	0.00 RPM
SRP009831_embryo	0.15 RPM	0.00 RPM
SRP009831_heart	0.05 RPM	0.00 RPM
SRP009831_liver	0.00 RPM	0.00 RPM
SRP009831_lung	0.50 RPM	0.05 RPM
SRP009831_ovary	0.00 RPM	0.00 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_196 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_196 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000026874	1 retrocopy	retro_acar_196 ,