RetrogeneDB ID: retro_acar_167

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343258.1:829503..830203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000024488
• Aliases: None
• Description: None

Sequence

>retro_acar_167
AATAATTTGAGATTGCTCAAGAGCTTAAAAGAGGATATGGATATTTTCTGTAGTCTGCAACATGGTCAACAGTCTCTTAG
AAAAAGCCAGGGAGATGCACAAAGAATCTGTGAAAGAATTTCAGGAGAACTTTGACACAGCAAGATCAGTGGTGGAGTCT
ATGGGTGGAGAAGTTAGGATTCCTCACATCTGTTCAAGGCAAACTTGTAAAAGCAATATCCAGACAATTTTACCAACACC
AATGGAATATTACAGGCTAAATGTGTACATCCCATTTCTGGACTATTTCTGCAGTCAGCTTCAAGAAAGGTTTACAAGGC
CTAGGTAAGGAATTCAGGAACTACAACTATTCCTACCTATTAATTGTGGCCATTTAAAATCCAACTTGAACAAGTGCACG
TAACTTTACAATGAATGCCTTGAAGACTAACACACTGATAGAAGAGTTTGACCTGTGGTGTATAAAATTGGAAAAAAGAT
TACACCTGCAGAGAAACCATCATATGCACTGGAAGCATATCTTGTTTGTGATAGACATTTTTTTCCAAATGTGAAGAAAC
TTCTTCAGATTTCTGCAACATTGCCAGGGTCAACAGCTACAAATGAAAGGTCATTTTCAATTCTTAAATGTTTGAAAACA
TACATAAGTAGCACAATGGGGTAAGAAAGACTAACTAGACTTGCACTCTTGAGTATCCAC

Alignment

ORF - retro_acar_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 53.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSLQLSKTLQRVDVDIFGSLQH-VDSLLEKAREMHTESVKEFQEIFDTARSVMESMGGEVRIPRICSRQT
          ..L.L.K.L...D.DIF.SLQH.V.SLLEKAREMH.ESVKEFQE.FDTARSV.ESMGGEVRIP.ICSRQT
Retrocopy NNLRLLKSLKE-DMDIFCSLQH>VNSLLEKAREMHKESVKEFQENFDTARSVVESMGGEVRIPHICSRQT

Parental  CQSNIQATSPTPMEYYRLNVYILFLDFFCSQFQERFTRHREVVQELQVFLPINCGHLKPNLNKCTELYNE
          C.SNIQ...PTPMEYYRLNVYI.FLD.FCSQ.QERFTR.R...QELQ.FLPINCGHLK.NLNKCT.LYNE
Retrocopy CKSNIQTILPTPMEYYRLNVYIPFLDYFCSQLQERFTRPR*GIQELQLFLPINCGHLKSNLNKCT*LYNE

Parental  FLQDSDTLMEEFDMWCRKWKKIAPAEKPSNALEADHDLIPMLEYFPYAWGFLQ---TLPVSTATNEGSFS
          .L.D..T............KKI.PAEKPS.ALEA...L......FP.....LQ...TLP.STATNE.SFS
Retrocopy CLED*HTDRRV*PVVYKIGKKITPAEKPSYALEA--YLVCDRHFFPNVKKLLQISATLPGSTATNERSFS

Parental  TLKCLKTYTRSTMRQERLTELARLSVH
          .LKCLKTY..STM..ERLT.LA.LS.H
Retrocopy ILKCLKTYISSTMG*ERLTRLALLSIH

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	0.07 RPM
SRP009831_brain	0.00 RPM	0.05 RPM
SRP009831_dewlap	0.00 RPM	0.00 RPM
SRP009831_embryo	0.00 RPM	0.00 RPM
SRP009831_heart	0.00 RPM	0.00 RPM
SRP009831_liver	0.00 RPM	0.00 RPM
SRP009831_lung	0.00 RPM	0.30 RPM
SRP009831_ovary	0.00 RPM	0.00 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_167 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_167 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000024488	1 retrocopy	retro_acar_167 ,
Bos taurus	ENSBTAG00000031609	2 retrocopies	retro_btau_1797, retro_btau_780,
Canis familiaris	ENSCAFG00000005274	1 retrocopy	retro_cfam_663,
Equus caballus	ENSECAG00000021982	1 retrocopy	retro_ecab_150,
Homo sapiens	ENSG00000137492	1 retrocopy	retro_hsap_4080,
Mustela putorius furo	ENSMPUG00000008784	1 retrocopy	retro_mputfur_1571,
Pan troglodytes	ENSPTRG00000004091	1 retrocopy	retro_ptro_2766,
Tursiops truncatus	ENSTTRG00000013287	1 retrocopy	retro_ttru_126,