RetrogeneDB ID: retro_acar_72

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:225574868..225575264(-)
• Located in intron of: ENSACAG00000010505

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000028327
• Aliases: None
• Description: None

Sequence

>retro_acar_72
ATGTTGTTGGGCATGGAGGCCAAGGGCAGCGGCGGGTCTCGCGCCTGCAGGAAGCTCATTGCGGCCGAAGAGGCCGAGTT
GTTCGAGCTCGCGCAGGCAGCAGGGAGCGCGCTTGACCTGGAAGTGTTCAAGATCCTGCTGGGTCTGGTGCTCATGAATG
TGGCCCCTGTGGCCACCTTCCAGATGCTGTGTGCTATGTGTGCTGCCAGGTAGAGAGAAAGTGGCCCTGAGGCCAATGCC
ACCAAGCCCCCGCAAGGTAGACCCAGAACTATATCTGCAACATCTGGGAACCAGACGCTGTCAGACCATAGTAGCCGGGA
AGGATCTATTCAACAAGTACCTTGGCAACCAAGTGCCAGCAGGTTACAGAAGGCTGGATGCTCTGGGAAAAGTGCA

Alignment

ORF - retro_acar_72 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSGMEAKGSGGSRARRKLLTAEEAELFELAQAAGTGLDPEVFKILLDLLRMNVAPVAIYQVLRAMCAAG
          M..GMEAKGSGGSRA.RKL..AEEAELFELAQAAG..LD.EVFKILL.L..MNVAPVA..Q.L.AMCAA.
Retrocopy MLLGMEAKGSGGSRACRKLIAAEEAELFELAQAAGSALDLEVFKILLGLVLMNVAPVATFQMLCAMCAAR

Parental  QRVSGPEANATEPPRGRPRTISATSGNQTLSDQSSREGSIQRVPRQPSASRLQKAGCPGKSA
          .R.SGPEANAT.PP.GRPRTISATSGNQTLSD.SSREGSIQ.VP.QPSASRLQKAGC.GKSA
Retrocopy *RESGPEANATKPPQGRPRTISATSGNQTLSDHSSREGSIQQVPWQPSASRLQKAGCSGKSA

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	0.62 RPM	9.85 RPM
SRP009831_brain	0.33 RPM	19.84 RPM
SRP009831_dewlap	0.00 RPM	8.77 RPM
SRP009831_embryo	0.33 RPM	26.82 RPM
SRP009831_heart	0.16 RPM	11.00 RPM
SRP009831_liver	0.25 RPM	13.46 RPM
SRP009831_lung	0.65 RPM	4.99 RPM
SRP009831_ovary	0.04 RPM	14.83 RPM
SRP009831_skeletal_muscle	0.18 RPM	11.62 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_72 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_72 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	ENSACAG00000028327	1 retrocopy	retro_acar_72 ,