RetrogeneDB ID: retro_acar_88

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:41302572..41302917(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSACAG00000003875
• Aliases: None
• Description: None

Sequence

>retro_acar_88
AGCAGCGGGTGGATCCGGGCAAGCAGGGTATTAACATCTTTTGGCACTCCTCTTTTCTGTAATATTCATACAAGTGCATC
TCTTGGGAATTTGGGAAGATGGGAAAAAAAGAATAGAGTTGTTTATCCCCCACAGCAGCCAGGAGAACCTCGAAGACCTG
CAGAAATATATCACTGTCGAAGAGATATTAAATACAGCAAGGACAAGATGTGGTACCTGGCAAAATTGATACGTGGAATG
ACCATTGATGAGGCACTAGCTCAGTTGGAATTCAATGATAAAAAAGGAGCAAAGGTAATGAAAGAGGTCCTTCTGGAAGC
ACAAGAAATGGCAGTGAGAACATGT

Alignment

ORF - retro_acar_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.04 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSLFILSFRVLTSFGTPLFCNIHTSASLGNLGRWEKKNRVVYPPQQPGEPRRPAEIYHCRRDIKYSKDKM
          .S..I...RVLTSFGTPLFCNIHTSASLGNLGRWEKKNRVVYPPQQPGEPRRPAEIYHCRRDIKYSKDKM
Retrocopy SSGWIRASRVLTSFGTPLFCNIHTSASLGNLGRWEKKNRVVYPPQQPGEPRRPAEIYHCRRDIKYSKDKM

Parental  WYLAKLIRGMTIDEALAQLEFNDKKGAKVIKEVLLEAQEMAVRKC
          WYLAKLIRGMTIDEALAQLEFNDKKGAKV.KEVLLEAQEMAVR.C
Retrocopy WYLAKLIRGMTIDEALAQLEFNDKKGAKVMKEVLLEAQEMAVRTC

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	3.61 RPM	24.81 RPM
SRP009831_brain	2.51 RPM	9.18 RPM
SRP009831_dewlap	1.94 RPM	6.29 RPM
SRP009831_embryo	7.23 RPM	29.19 RPM
SRP009831_heart	4.36 RPM	11.83 RPM
SRP009831_liver	3.89 RPM	22.66 RPM
SRP009831_lung	1.21 RPM	13.35 RPM
SRP009831_ovary	1.74 RPM	8.42 RPM
SRP009831_skeletal_muscle	2.26 RPM	8.96 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_88 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_88 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88 ,
Bos taurus	ENSBTAG00000019457	1 retrocopy	retro_btau_1348,
Canis familiaris	ENSCAFG00000017605	2 retrocopies	retro_cfam_1456, retro_cfam_584,
Callithrix jacchus	ENSCJAG00000007325	2 retrocopies	retro_cjac_2187, retro_cjac_2558,
Homo sapiens	ENSG00000082515	1 retrocopy	retro_hsap_3041,
Gorilla gorilla	ENSGGOG00000010232	1 retrocopy	retro_ggor_2095,
Macaca mulatta	ENSMMUG00000021229	1 retrocopy	retro_mmul_1889,
Mus musculus	ENSMUSG00000020514	1 retrocopy	retro_mmus_1294,
Nomascus leucogenys	ENSNLEG00000016692	1 retrocopy	retro_nleu_1928,
Otolemur garnettii	ENSOGAG00000016777	1 retrocopy	retro_ogar_1042,
Pongo abelii	ENSPPYG00000015979	1 retrocopy	retro_pabe_2436,
Pan troglodytes	ENSPTRG00000017453	1 retrocopy	retro_ptro_1997,
Vicugna pacos	ENSVPAG00000001170	1 retrocopy	retro_vpac_294,