RetrogeneDB ID: retro_acar_204

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344877.1:10749..11001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSACAG00000029331
• Aliases: None
• Description: None

Sequence

>retro_acar_204
CAGGAACAACTGCCAACTGTCCCTTTATCAAACATGTACAAGAAGTCTGGTGGAAAAGTCCGACTCACTTTCAAACTCGA
ACAGGATCAGCTCTGGATTGGCACTAAAGAAAGGACAGAAAAGTTACCAATGGGGTCCATCAAGAACGTGGTGAGCGAAC
CCATTGAAGGACATGAGGATTATCACATGATGGCCTTCCAGCTGGGGTCGACAGAGACCTCCTACTACTGGGTCTACTGG
ATCCCCACCCAA

Alignment

ORF - retro_acar_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 62.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QERLPTVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEGHEDYHMMAFQLGP
          QE.LPTVPLS.MY.KSGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEGHEDYHMMAFQLG.
Retrocopy QEQLPTVPLSNMYKKSGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEGHEDYHMMAFQLGS

Parental  TEASYYWVYWVPTQ
          TE.SYYWVYW.PTQ
Retrocopy TETSYYWVYWIPTQ

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	7.48 RPM
SRP009831_brain	0.00 RPM	5.68 RPM
SRP009831_dewlap	0.00 RPM	66.44 RPM
SRP009831_embryo	0.00 RPM	7.68 RPM
SRP009831_heart	0.00 RPM	14.27 RPM
SRP009831_liver	0.00 RPM	8.47 RPM
SRP009831_lung	0.00 RPM	14.51 RPM
SRP009831_ovary	0.08 RPM	79.11 RPM
SRP009831_skeletal_muscle	0.00 RPM	32.96 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_204 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_204 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204 ,
Canis familiaris	ENSCAFG00000017670	1 retrocopy	retro_cfam_1952,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372,
Cavia porcellus	ENSCPOG00000006872	2 retrocopies	retro_cpor_292, retro_cpor_635,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,
Oryctolagus cuniculus	ENSOCUG00000008444	1 retrocopy	retro_ocun_666,
Pongo abelii	ENSPPYG00000007191	1 retrocopy	retro_pabe_2528,