RetrogeneDB ID: retro_acar_116

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:9804793..9805003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB6
• Ensembl ID: ENSACAG00000001263
• Aliases: None
• Description: None

Sequence

>retro_acar_116
TGGCGGGCTGTGGAGGAGACCTACAAAGTTGGAGCATTTGTTTTCACTGGAATACTTGTTCCTTTTTGGCTTACTCACCA
CTACGTAAAATACCACCTGCTGTATCAGCCATATGGAGTTGTCGTCTCCAAGCCCAAGATATTCCCAGGTGACATTATTC
TGGAGACGAATGAAGTTGTTCCTCCATTAGAAATACCAGACAGTCATCAT

Alignment

ORF - retro_acar_116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WRTQVYKTYKAGAFVFTGILVPFWLTHYYVKYHLLYQPYGAVVSKPKIFPGDTILETKEVVPPLEIPDSH
          WR..V..TYK.GAFVFTGILVPFWLTH.YVKYHLLYQPYG.VVSKPKIFPGD.ILET.EVVPPLEIPDSH
Retrocopy WRA-VEETYKVGAFVFTGILVPFWLTHHYVKYHLLYQPYGVVVSKPKIFPGDIILETNEVVPPLEIPDSH

Parental  H
          H
Retrocopy H

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	0.03 RPM	108.51 RPM
SRP009831_brain	0.00 RPM	103.67 RPM
SRP009831_dewlap	0.00 RPM	80.11 RPM
SRP009831_embryo	0.00 RPM	79.52 RPM
SRP009831_heart	0.05 RPM	128.72 RPM
SRP009831_liver	0.00 RPM	141.77 RPM
SRP009831_lung	0.00 RPM	75.11 RPM
SRP009831_ovary	0.04 RPM	84.75 RPM
SRP009831_skeletal_muscle	0.00 RPM	127.59 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_116 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_116 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001263	3 retrocopies	retro_acar_110, retro_acar_116 , retro_acar_117,
Callithrix jacchus	ENSCJAG00000007852	3 retrocopies	retro_cjac_1287, retro_cjac_255, retro_cjac_303,
Dasypus novemcinctus	ENSDNOG00000019864	2 retrocopies	retro_dnov_2281, retro_dnov_920,
Ochotona princeps	ENSOPRG00000007428	5 retrocopies	retro_opri_148, retro_opri_525, retro_opri_591, retro_opri_614, retro_opri_722,
Sus scrofa	ENSSSCG00000011003	1 retrocopy	retro_sscr_260,
Tupaia belangeri	ENSTBEG00000013268	2 retrocopies	retro_tbel_195, retro_tbel_197,
Tarsius syrichta	ENSTSYG00000002785	1 retrocopy	retro_tsyr_382,
Tursiops truncatus	ENSTTRG00000012172	1 retrocopy	retro_ttru_1505,