RetrogeneDB ID: retro_acar_159

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343209.1:1225285..1225795(-)
• Located in intron of: ENSACAG00000008892

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCSTN
• Ensembl ID: ENSACAG00000016223
• Aliases: None
• Description: None

Sequence

>retro_acar_159
CATGTAGTGGAGAAGGAAGCAGATTTGAAGTGGGTGCTTATGGATGGGCTACATGCCCCTTATGTGATGCTGCTGGATGG
AGAACTGTTCACTGGAGAATGGATACGGAGGTTGAAAGGCAGCTCTCGGATTTCTGGGCTAGTAGTAGCCATTGCCAAGC
CCAGCCCTTCTAGAGGGGTTTCTCTTGGCTTACAATGTCCCAATGATGGCTTTGGCATCTACAGTGATAGTTACGGCCCT
GAATATGCACACTGCAGCCCCACTGTCTGGAACCTTCTCGGCAGCGGCCTTTCCTATGAGGACTTTGACTTTCCCATTTT
CCTTCTTCAAGATAAGAATGAAACAGAGGTCATCAAGCAGTGCTACCATACCTACAACCACACTCAATATAACTCCATCC
CGCAGTATCTGCTGTGCGCCATGCAGCTGTCTTCCCACATGCATGCAATTACAAGCACAGCCACATGTATGCGCTGCAGT
GCCATCCAGAGTACCTTCTGCTTCAACCCA

Alignment

ORF - retro_acar_159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HVVEDEEVDLKWVLEEGPHAPYVLLLDGELFTGELMQRLKGSSRISGLAVAIAKPSPSRGFSPGLKCPND
          HVVE..E.DLKWVL..G.HAPYV.LLDGELFTGE...RLKGSSRISGL.VAIAKPSPSRG.S.GL.CPND
Retrocopy HVVE-KEADLKWVLMDGLHAPYVMLLDGELFTGEWIRRLKGSSRISGLVVAIAKPSPSRGVSLGLQCPND

Parental  GFGVYNGSYGPEFAHCNVTAWNLLGNGLSYQDFGFPIFLLQDQNETEVIKQCFQTYNRPRGGSAPQYPLC
          GFG.Y..SYGPE.AHC..T.WNLLG.GLSY.DF.FPIFLLQD.NETEVIKQC..TYN.....S.PQY.LC
Retrocopy GFGIYSDSYGPEYAHCSPTVWNLLGSGLSYEDFDFPIFLLQDKNETEVIKQCYHTYNHTQYNSIPQYLLC

Parental  AMQLSSHMHAVTSTVTCMRRSAIQSTFSLNP
          AMQLSSHMHA.TST.TCMR.SAIQSTF..NP
Retrocopy AMQLSSHMHAITSTATCMRCSAIQSTFCFNP

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	4.40 RPM
SRP009831_brain	0.09 RPM	11.41 RPM
SRP009831_dewlap	0.13 RPM	21.64 RPM
SRP009831_embryo	0.06 RPM	17.58 RPM
SRP009831_heart	0.10 RPM	18.06 RPM
SRP009831_liver	0.08 RPM	9.86 RPM
SRP009831_lung	0.71 RPM	13.65 RPM
SRP009831_ovary	0.00 RPM	28.65 RPM
SRP009831_skeletal_muscle	0.04 RPM	5.65 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_159 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_159 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016223	1 retrocopy	retro_acar_159 ,
Anolis carolinensis	ENSACAG00000022172	1 retrocopy	retro_acar_158,