RetrogeneDB ID: retro_acar_200

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343742.1:154226..154695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSACAG00000028556
• Aliases: None
• Description: cell division cycle associated 8 [Source:HGNC Symbol;Acc:14629]

Sequence

>retro_acar_200
ATGGCTCCTTCAAAGAAGAAAAGGTCAAAGGCATCAAGCAAGATAGATGTCCTTCAGGGACAAACATAGCGATGCGTTCC
TCAAGGCCTTTGACCAAGAAGTTCAAAGCCGCATCGAGTAACTCAGGGCGGACTTCAAGAACCTGCAGGGGAATATAAGC
ACCATGTTCAACCAGGAGATGCTGCGCCTGCCCACCGCCCTCCGGGAGATGAACTGGATCAGCTACTGAGCCTTCGGAGA
AGACCCGGCAGCCCTGGAGCAGCTTGCCTTGGAGCGAGCAGACTTCCAGGAAATTCACGAAATGGCCTCCAAGGCTTTGA
GGACCCCTGTCTGAACTGTCTGGAAAGCTGTGAAGGCCAAGCTGCCCATCGAGAGCATCAAGGAGGTGGAGGGCCCCGTC
CTGCACATGAGGAAGAGGTCGCAGCAGGAGGAGGAGGAGGAGGAGGAGGCCCCCACCCCCCTCTCTCCG

Alignment

ORF - retro_acar_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSKK-KRSKAQSK-NSLRDKQIDAFIESFDQEVKRRVEKLRADLKNVQENISTMFDREILRLPTALRE
          MAPSKK.K....Q....S.RDK..DAF...FDQEV..R.E.LRAD.KN.Q.NISTMF..E.LRLPTALRE
Retrocopy MAPSKK>KGQRHQAR*MSFRDKHSDAFLKAFDQEVQSRIE*LRADFKNLQGNISTMFNQEMLRLPTALRE

Parental  MNWISYCALGEDPAVLEQLALEGTDVQEINEMASKALRTPVRTVRKAAKAKLPIESIEEEEEGPILPLRK
          MNWISY.A.GEDPA.LEQLALE..D.QEI.EMASKALRTPV.TV.KA.KAKLPIESI..E.EGP.L..RK
Retrocopy MNWISY*AFGEDPAALEQLALERADFQEIHEMASKALRTPV*TVWKAVKAKLPIESI-KEVEGPVLHMRK

Parental  RSRQEDEAPIPLPPEQKP
          RS..........P....P
Retrocopy RSQXXXXXXXXXPTPLSP

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	2.00 RPM
SRP009831_brain	0.00 RPM	0.33 RPM
SRP009831_dewlap	0.08 RPM	10.59 RPM
SRP009831_embryo	0.03 RPM	79.52 RPM
SRP009831_heart	0.00 RPM	0.93 RPM
SRP009831_liver	0.00 RPM	4.50 RPM
SRP009831_lung	0.00 RPM	1.96 RPM
SRP009831_ovary	0.12 RPM	31.85 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.07 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_200 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_200 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200 ,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594, retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746,