RetrogeneDB ID: retro_acar_119

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:50180051..50180500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYBASC3
• Ensembl ID: ENSACAG00000017746
• Aliases: None
• Description: None

Sequence

>retro_acar_119
TCTGTCAAGCTGAGGAACTATGCTTCCCAGCATCCCCAGTGGTGCAGGGAGAAGGCAGAAGATGTGCTCCATAGTAGCAG
TGCAATGTCTGGTATCCCATTCTTGCCATTTTCCATCCTACTTGGAGCTCTGGGAATCTTGTGCATGGGCTTCACAGTGT
ATTGGAGTTACCACTGGCTTGGTGGCTTTGCCTGTGATTAATCAGCTCAGATGTTTAACTGGCACCCAGTTCTCATGGTG
ACAGGCATGTTGGCCTTGTATGGGGCTGCAGCACTGGAATATCAGGTGCCTTCTCCTGGCAGGGATTCAAGCTCTCATGG
AAGCTACTACATGCATCTCTGACCTTGAAAGCATCCATTACTGTTGTCCTGAGACTAATAGCTGTCTTTGAATATCACAA
TGTGCAGGGGATCCCAAACATGTACTCACTACGCAGCGGAATAGGTCTG

Alignment

ORF - retro_acar_119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.47 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVELRNYVSRHPPRRRQKAEDVLHSSSVMPDIPFLPFSILLGVLGILCVGFTVYWSHHWLDGFAWDGSAQ
          SV.LRNY.S.HP...R.KAEDVLHSSS.M..IPFLPFSILLG.LGILC.GFTVYWS.HWL.GFA.D.SAQ
Retrocopy SVKLRNYASQHPQWCREKAEDVLHSSSAMSGIPFLPFSILLGALGILCMGFTVYWSYHWLGGFACD*SAQ

Parental  MFNWHPVLMVTGMLVLYGAAALVYRVP-LSWQGSKLPWKLVHASLTLTASIIVVLGLVAVFEYHNVQGIP
          MFNWHPVLMVTGML.LYGAAAL.Y.VP..SWQG.KL.WKL.HASLTL.ASI.VVL.L.AVFEYHNVQGIP
Retrocopy MFNWHPVLMVTGMLALYGAAALEYQVP<FSWQGFKLSWKLLHASLTLKASITVVLRLIAVFEYHNVQGIP

Parental  NMYSLHSWVGL
          NMYSL.S..GL
Retrocopy NMYSLRSGIGL

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	140.15 RPM
SRP009831_brain	0.00 RPM	1.66 RPM
SRP009831_dewlap	0.00 RPM	22.53 RPM
SRP009831_embryo	0.00 RPM	7.11 RPM
SRP009831_heart	0.00 RPM	1.09 RPM
SRP009831_liver	0.00 RPM	4.50 RPM
SRP009831_lung	0.00 RPM	3.88 RPM
SRP009831_ovary	0.00 RPM	24.25 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.84 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_119 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_119 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	ENSACAG00000017746	1 retrocopy	retro_acar_119 ,