RetrogeneDB ID: retro_acar_24

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343232.1:331658..331976(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000000473
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000015604
• Aliases: None
• Description: None

Sequence

>retro_acar_24
GTCACCCCAAAGGCGTGGAAGATGAAGTGTGGCGGGACCTCAGAGACCAAGCCAGCCACTGAAGAGACACAGCAGATTGT
CCAGCACGTCAAGGCCCAAGTGGAAGAGAAAGAAGGCAAGAGCTTTGATGTCTTCACTGCAGTCGAGTTTAAAACCCAGA
TGGTTGCTGGAATAAACTACTTCATCAAGGTCCATGTTGGGAATGACCAATTCCTTCATGTGCGAATCTTCAAAAGCCTC
CCTCATGAGAACAAGCCACCGGAGCTCACCAGCTACCAAAGCAAGAAAGGAAAGCACGATGAACTGTCCTATTTCTAG

Alignment

ORF - retro_acar_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAGGLSEVKPATPEIQEMVDQTKGEIEKKENKTYSIFKAIEYRTQLVSGTNYFIKVD-GGKEYLHVRIY
          M..GG.SE.KPAT.E.Q..V...K...E.KE.K....F.A.E..TQ.V.G.NYFIKV..G....LHVRI.
Retrocopy MKCGGTSETKPATEETQQIVQHVKAQVEEKEGKSFDVFTAVEFKTQMVAGINYFIKVHVGNDQFLHVRIF

Parental  KPLPQSGEKPSLTSYQTGKTASDPLIYF
          K.LP.....P.LTSYQ..K...D.L.YF
Retrocopy KSLPHENKPPELTSYQSKKGKHDELSYF

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	58.29 RPM	0.07 RPM
SRP009831_brain	38.30 RPM	0.00 RPM
SRP009831_dewlap	24.68 RPM	3.71 RPM
SRP009831_embryo	45.64 RPM	0.15 RPM
SRP009831_heart	45.03 RPM	4.62 RPM
SRP009831_liver	144.10 RPM	3.68 RPM
SRP009831_lung	96.72 RPM	0.10 RPM
SRP009831_ovary	19.92 RPM	0.35 RPM
SRP009831_skeletal_muscle	22.62 RPM	0.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_24 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_24 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015604	1 retrocopy	retro_acar_24 ,
Mus musculus	ENSMUSG00000034362	1 retrocopy	retro_mmus_56,
Pteropus vampyrus	ENSPVAG00000012705	3 retrocopies	retro_pvam_230, retro_pvam_601, retro_pvam_624,