RetrogeneDB ID: retro_acar_64

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:21213690..21214062(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GFER
• Ensembl ID: ENSACAG00000012106
• Aliases: None
• Description: None

Sequence

>retro_acar_64
AAAAACTGGATATGGGGGCAGAAGAGGCAGGGCGCCGTGGAAGCCAGAGCTGAATTGAAAGAGTACCCCCCGGACTGTCC
TCTGGATTGGGAGCAGCTGGAGAGGAGCTCCTGGTCCTTCCTTCATACAATGGCAGCTTACTACCACAACCAGTCCAATA
CAAGCGAGCAGGAGGAAATGGTCCAGTTCATCAACTTATTTCCAAGGTTCTCCCTTGTAACGAATGTGGATTAGATTTTA
GGAAAATGATACAACGGAATCAGCCCAGCGCCTCCAGCAGGCACAATCTGACATAATGGATTTTGCTGGATCCACAATGA
GGTGAACCAGAAACTGGGGAAGCCCGAATTTGACTGTTCCCTCATCGATGAG

Alignment

ORF - retro_acar_64 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 74.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSWMREQKRQGAAEIGAELKENPLNCPLDREELGRNSWSFLHTMAAYYPDRPNKTEQQEMIQFINLF-SK
          ..W...QKRQGA.E..AELKE.P..CPLD.E.L.R.SWSFLHTMAAYY....N..EQ.EM.QFINLF.SK
Retrocopy KNWIWGQKRQGAVEARAELKEYPPDCPLDWEQLERSSWSFLHTMAAYYHNQSNTSEQEEMVQFINLF<SK

Parental  VFPCEECREDFRKRIQQNQPDASSQRNLTQW-FCRIHNEVNQKLGKPEFDCSLVDE
          V.PC.EC..DFRK.IQ.NQP.ASS..NLT.W.FC.IHNEVNQKLGKPEFDCSL.DE
Retrocopy VLPCNECGLDFRKMIQRNQPSASSRHNLT*W>FCWIHNEVNQKLGKPEFDCSLIDE

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	11.78 RPM
SRP009831_brain	0.00 RPM	10.32 RPM
SRP009831_dewlap	0.00 RPM	42.78 RPM
SRP009831_embryo	0.00 RPM	25.22 RPM
SRP009831_heart	0.00 RPM	13.18 RPM
SRP009831_liver	0.00 RPM	15.67 RPM
SRP009831_lung	0.00 RPM	22.67 RPM
SRP009831_ovary	0.00 RPM	42.62 RPM
SRP009831_skeletal_muscle	0.00 RPM	25.31 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_64 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_64 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	ENSACAG00000012106	1 retrocopy	retro_acar_64 ,