RetrogeneDB ID: retro_acar_157

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343203.1:1196799..1197249(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDE6D
• Ensembl ID: ENSACAG00000012101
• Aliases: None
• Description: None

Sequence

>retro_acar_157
CAGGAAGAGGAAGAGCAGGCCAAGGGGATCCTGGAGGGATTCAATCTAAATTGAATGAGCCCCCAGGATGCCGAAACAGA
GAAAATTCTTTGGCAAGGAACAGAAGACGTCTCCATCTCTGGAGTCAAGCATAATTCTCATGTCCCAAAGAAAATTTTAA
AATGCTAAGCTGTCTCTCAGGAGCTAAACTTTTCATCAACTGAGCCAATGGAGAAATTCTGACTGGAACAGAAAGTGCAT
TTCAAAGGACAGTGTTTTGAAGGAAGGTTCTCTGAGTTTGGCTTTGTGACTCCTAACTCCACAAACACCTGGCAGTCCTT
GATAGAAGCGGCTCCCGAGTCAAAGATAATACCTGCTAATGTTCTAACCAGGAACATTATCATAGAAACCAAGTTTTTCA
ACAACAACAACCTTTTTTAAAGCATTTCCAGAGTAAGACTCTTCCACGTT

Alignment

ORF - retro_acar_157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEEERAKEILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQM
          .EEEE.AK.IL.GF.LN.M...DAET.KILWQGTED.S..GV.H...VPKKILKC.AVS.ELNFSSTE.M
Retrocopy QEEEEQAKGILEGFNLN*MSPQDAETEKILWQGTEDVSISGVKHNSHVPKKILKC*AVSQELNFSSTEPM

Parental  EKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPANVLTGNVIIETKFF-DDDLLV
          EKF.LEQKV.FKGQC.E..F.EFGFV.PNSTNTWQSLIEAAPES...PANVLT.N.IIETKFF....L..
Retrocopy EKF*LEQKVHFKGQCFEGRFSEFGFVTPNSTNTWQSLIEAAPESKIIPANVLTRNIIIETKFFNNNNLF*

Parental  STSRVRLFYV
          S.SRVRLF.V
Retrocopy SISRVRLFHV

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	20.28 RPM
SRP009831_brain	0.00 RPM	52.69 RPM
SRP009831_dewlap	0.00 RPM	66.36 RPM
SRP009831_embryo	0.00 RPM	32.99 RPM
SRP009831_heart	0.00 RPM	37.25 RPM
SRP009831_liver	0.00 RPM	19.35 RPM
SRP009831_lung	0.00 RPM	27.76 RPM
SRP009831_ovary	0.00 RPM	67.53 RPM
SRP009831_skeletal_muscle	0.00 RPM	16.21 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_157 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_157 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012101	1 retrocopy	retro_acar_157 ,
Dasypus novemcinctus	ENSDNOG00000000568	1 retrocopy	retro_dnov_2585,
Felis catus	ENSFCAG00000002232	1 retrocopy	retro_fcat_317,
Macropus eugenii	ENSMEUG00000006427	1 retrocopy	retro_meug_1355,
Oryctolagus cuniculus	ENSOCUG00000010403	1 retrocopy	retro_ocun_182,
Pteropus vampyrus	ENSPVAG00000004743	1 retrocopy	retro_pvam_544,
Tursiops truncatus	ENSTTRG00000009165	1 retrocopy	retro_ttru_82,