RetrogeneDB ID: retro_acar_87

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:199515441..199515795(+)
• Located in intron of: ENSACAG00000017226

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000024337
• Aliases: None
• Description: None

Sequence

>retro_acar_87
TATCCTAATTCTGATGTCCTTCTTGCAGAGAAGCCAGAAGTGAAGGTGACACGCAAGGAGGACTATGATGGGATGGAGAC
CCTGACCTGTCATGTTGGCGGCTTTTACCCCAAGGAGATTGACATCACCTGGACAAAGGATGGGGAGGACAGGCGTCAGG
ATGTCTTCCATGGCCTGGTGTCCCCCAACTCAGATGGGACTTACTACACCTGGTGGAGCATCACGGTGGACCCCAAGGAG
AGGGAACGCTACAAATGCCACGTGGAGCACGATGGGCTTCTTAACCCCATGGACGTGGTCTGGGAGGCGTGTGGTGAGTC
ATTTGAGAGGAGGATTATGGGAAGGACAAGAGGA

Alignment

ORF - retro_acar_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 86.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPNSDVILAEKPEVKVTRKVDYDGMETLICWVGGFYPKEIDIITWTKDGEDRQQDTFHGLVSPNSDGTYY
          YPNSDV.LAEKPEVKVTRK.DYDGMETL.C.VGGFYPKEIDI.TWTKDGEDR.QD.FHGLVSPNSDGTYY
Retrocopy YPNSDVLLAEKPEVKVTRKEDYDGMETLTCHVGGFYPKEIDI-TWTKDGEDRRQDVFHGLVSPNSDGTYY

Parental  TWRSITVDPKERECYKCHVEHDGLLNPVDVAWEEPDSASKSVLIGCAMG
          TW.SITVDPKERE.YKCHVEHDGLLNP.DV.WE...........G...G
Retrocopy TWWSITVDPKERERYKCHVEHDGLLNPMDVVWEACGESFERRIMGRTRG

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	4.73 RPM	0.10 RPM
SRP009831_brain	0.33 RPM	0.00 RPM
SRP009831_dewlap	0.08 RPM	0.00 RPM
SRP009831_embryo	0.09 RPM	0.00 RPM
SRP009831_heart	1.66 RPM	0.00 RPM
SRP009831_liver	2.66 RPM	0.08 RPM
SRP009831_lung	2.32 RPM	0.00 RPM
SRP009831_ovary	0.04 RPM	0.00 RPM
SRP009831_skeletal_muscle	0.66 RPM	0.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_87 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_87 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	ENSACAG00000024337	1 retrocopy	retro_acar_87 ,