RetrogeneDB ID: retro_acar_160

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343210.1:1869358..1869720(+)
• Located in intron of: ENSACAG00000001021

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2ORF72
• Ensembl ID: ENSACAG00000022814
• Aliases: None
• Description: None

Sequence

>retro_acar_160
CTGCTACGGAGTGTCTTCCGGGAGATGAAAGGAGCCGCCGCGGAGGAGACCCTGCAAGCCGCACTCTACATGCCCGGAGG
AAGAGGAGGAGGAGGAGCGGCCCAGGTCGAGGAGGCTGCGTGCAAGACACTCAGCGCCACCCTCAGGATTCAAGCAGATG
GGGTGGAAATCGAGACACAGAAGCTCCCTTTCTTCTTGCAGTGCCTTCCGTGGGGCAGAAGGAGACAGCAGAGAAAAGGC
AGTTGGAGACAGGAGCAAACAAGGTTAAGCAAGATGCCTCTCAAGATGCAGAAGAAGTCATGGCTTTGACTAGCATGGCA
CCTAATGGGAATTGTGAAGATGCCTGTGGAAAGGCAGGCATT

Alignment

ORF - retro_acar_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.79 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRGVFRERKGAAAEETLQAALYDPGG-GGGGAGQVQEAACKALSAALSIHADGVEIETQKLPFFLQCLP
          LLR.VFRE.KGAAAEETLQAALY.PGG.GGGGA.QV.EAACK.LSA.L.I.ADGVEIETQKLPFFLQCLP
Retrocopy LLRSVFREMKGAAAEETLQAALYMPGGRGGGGAAQVEEAACKTLSATLRIQADGVEIETQKLPFFLQCLP

Parental  WGRRRQRRKG-QLEADANYPKTDASQDAEEVVALTSMAPNGNCEDPCGKKRI
          WGRRRQ.RKG.QLE..AN..K.DASQDAEEV.ALTSMAPNGNCED.CGK..I
Retrocopy WGRRRQQRKG<QLETGANKVKQDASQDAEEVMALTSMAPNGNCEDACGKAGI

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	3.77 RPM
SRP009831_brain	0.09 RPM	4.12 RPM
SRP009831_dewlap	0.00 RPM	44.13 RPM
SRP009831_embryo	0.33 RPM	3.79 RPM
SRP009831_heart	0.16 RPM	4.05 RPM
SRP009831_liver	0.04 RPM	51.05 RPM
SRP009831_lung	0.76 RPM	5.84 RPM
SRP009831_ovary	0.04 RPM	55.36 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.36 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_160 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_160 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	ENSACAG00000022814	1 retrocopy	retro_acar_160 ,