RetrogeneDB ID: retro_acar_59

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:156124382..156124740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAP2
• Ensembl ID: ENSACAG00000028618
• Aliases: None
• Description: post-GPI attachment to proteins 2 [Source:HGNC Symbol;Acc:17893]

Sequence

>retro_acar_59
AACTGGAAAAAATCAAACAAGATGTTGCTTTTGACAAAGGTTTCTCTCTCAGCACACTCTTTAATATTCTCTGCACAGCA
TGAATGCATTTCTTTGCCCTCTGGCCTCTTTCTCTTTTTTGTTTGCTATTCTGACACTCCTGCGAACCCGAAATTCCAAA
TAGCCAGCTCGATCCAGAGATGCCATTCCATCAAGGCCAGATAGCTTGTTAGTAGCAGCCTCTGTCTGCTTGCTATCTAC
TGGGAAGCTGTCCTCCCTTTGCACCTGGCTAGTTTCAGTATCAACTCCCGTATTGTCAACATCATCCCCTGCCGTGGGAA
TGCCTCCCTGCTCTTCATCACTCACAACAGGAACACTC

Alignment

ORF - retro_acar_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.1 %
• Parental protein coverage: 50.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLMENLALLLLTYVSSSENYLIHES-AFILFIASALSHMFLTCILWRMTKKHTISPEPARSRDSVSSRPD
          N.......LLLT.VS.S...LI........F.....S..FL..IL.........S..PARSRD...SRPD
Retrocopy NWKKSNKMLLLTKVSLSAHSLIFSA>SMNAFLCPLASFSFLFAILTLLRTRN--SK*PARSRDAIPSRPD

Parental  SSLAAASVCTLSDWELSSLCTWLASVSSPVSTTSFPAMGMPPCSSSLTAGTL
          S.L.AASVC.LS...LSSLCTWL.SVS.PV..TS.PA.GMPPCSSSLT.GTL
Retrocopy SLLVAASVCLLSTGKLSSLCTWLVSVSTPVLSTSSPAVGMPPCSSSLTTGTL

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	0.00 RPM	1.77 RPM
SRP009831_brain	0.00 RPM	3.22 RPM
SRP009831_dewlap	0.00 RPM	1.86 RPM
SRP009831_embryo	0.00 RPM	13.19 RPM
SRP009831_heart	0.00 RPM	6.33 RPM
SRP009831_liver	0.00 RPM	2.05 RPM
SRP009831_lung	0.05 RPM	7.66 RPM
SRP009831_ovary	0.00 RPM	2.93 RPM
SRP009831_skeletal_muscle	0.00 RPM	3.50 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_59 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_59 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	ENSACAG00000028618	1 retrocopy	retro_acar_59 ,