RetrogeneDB ID: retro_acar_175

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343308.1:1041654..1042140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000014643
• Aliases: None
• Description: None

Sequence

>retro_acar_175
TCAAGCAGTCTGTCATCCTCGACAGGGAGTCCTTGTCCACTTTCTCCTTCAAAATCCACCACTTCTGCAAAGCCTCGTCC
ATGTGAGAAGAGAAATATGATTGCCAAAGCTAGAGAAGAAACTGGTTCCTTGAACCCAGTGCTGAAACTGGGGACCAAGC
AGAGCAGTATCATCATCAGTCTGTGTCAGCAAGGGAATCCCATCCTGAAATTCATCCGCAACGTGCCTTGGGAGTTTGGA
GACATCATCCCAGATTATTTGCTGAGCCAAAGCACCTGCACCCTTTTCCTAAGCCTCCACTACCACAACCTGAACCACAA
TTACATCCACGAATAGCTCTGCAACCTGAGAAAGACCTGTGCGCTGTAGGTGCTTCTGCTTCAGGTCGACATGAAAGATT
GACACCAGTTTCTCAAAGATCTGACCAAGATCTGCATCCTTTCCAGCTGCATTTTGATCCTGGCCTGGACCCCCAAAGAA
ATGGGC

Alignment

ORF - retro_acar_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSAPQAKQGTAGIPAAKSTTSAKPPPCEKRNIIAKGIGETSSSNPVLKPGTKQSSIIVSPRQRGNPVLK
          SSS..............KSTTSAKP.PCEKRN.IAK...ET.S.NPVLK.GTKQSSII.S..Q.GNP.LK
Retrocopy SSSLSSSTGSPCPLSPSKSTTSAKPRPCEKRNMIAKAREETGSLNPVLKLGTKQSSIIISLCQQGNPILK

Parental  FIRNVPWEFGDIVPDYLLGQSTCALFLSLRYHNLNPNYIHDRLRNLGKTYALQVLLLQVDVKDPHRALKD
          FIRNVPWEFGDI.PDYLL.QSTC.LFLSL.YHNLN.NYIH..L.NL.KT.AL.VLLLQVD.KD.H..LKD
Retrocopy FIRNVPWEFGDIIPDYLLSQSTCTLFLSLHYHNLNHNYIHE*LCNLRKTCAL*VLLLQVDMKD*HQFLKD

Parental  LAKICILSSCTLVLAWSPEEAG
          L.KICILSSC.L.LAW.P.E.G
Retrocopy LTKICILSSCILILAWTPKEMG

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	23.04 RPM
SRP009831_brain	0.00 RPM	16.52 RPM
SRP009831_dewlap	0.00 RPM	22.27 RPM
SRP009831_embryo	0.00 RPM	23.98 RPM
SRP009831_heart	0.00 RPM	63.04 RPM
SRP009831_liver	0.00 RPM	38.04 RPM
SRP009831_lung	0.00 RPM	39.64 RPM
SRP009831_ovary	0.00 RPM	19.81 RPM
SRP009831_skeletal_muscle	0.00 RPM	81.80 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_175 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_175 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014643	2 retrocopies	retro_acar_17, retro_acar_175 ,
Canis familiaris	ENSCAFG00000004448	1 retrocopy	retro_cfam_776,