RetrogeneDB ID: retro_acar_129

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:14821610..14821910(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSACAG00000006364
• Aliases: None
• Description: None

Sequence

>retro_acar_129
GTAAGTATTGAATTGAAGAATGGGACCCAGGTTCATGGAACCATCACAGGAGTGGATGTTAGTATGAATACACATCTGAA
AGCTGTGAAAATGACTCTGAAAAACAGAGAACATGTCCACTTGGAAACTTTGAATATTAGAGGCAATAATATTAGTTATT
TCATTCTGCCAGACAGCTTGCTGCTGGACACCCTCTTAGTGGATGTTGAACCAAAAGTCAAATCCAAGAAAAGGAAAGCA
GTTGCTTGAAGAGGACGTGGGAGAGGCAAACGACATGGCCAAGGAAGAGCAGGTCCAAGA

Alignment

ORF - retro_acar_129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85. %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVE
          V.IELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE.V.LETL.IRGNNI.YFILPDSL.LDTLLVDVE
Retrocopy VSIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREHVHLETLNIRGNNISYFILPDSLLLDTLLVDVE

Parental  PKVKSKKREAVAGRGRGRGRGRGRGRGRGR
          PKVKSKKR.AVA.RGRGRG...G.GR...R
Retrocopy PKVKSKKRKAVA*RGRGRGKRHGQGRAGPR

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	50.91 RPM
SRP009831_brain	0.00 RPM	43.32 RPM
SRP009831_dewlap	0.00 RPM	69.86 RPM
SRP009831_embryo	0.00 RPM	171.19 RPM
SRP009831_heart	0.00 RPM	21.01 RPM
SRP009831_liver	0.00 RPM	27.45 RPM
SRP009831_lung	0.00 RPM	13.80 RPM
SRP009831_ovary	0.00 RPM	69.49 RPM
SRP009831_skeletal_muscle	0.00 RPM	7.47 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_129 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_129 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 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129 ,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Homo sapiens	ENSG00000167088	2 retrocopies	retro_hsap_1147, retro_hsap_372,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Mus musculus	ENSMUSG00000002477	1 retrocopy	retro_mmus_1996,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Sarcophilus harrisii	ENSSHAG00000011791	1 retrocopy	retro_shar_147,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,