RetrogeneDB ID: retro_acar_97

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:85004795..85005126(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR4
• Ensembl ID: ENSACAG00000011328
• Aliases: None
• Description: signal sequence receptor, delta [Source:HGNC Symbol;Acc:11326]

Sequence

>retro_acar_97
GATGCGGCACTTTATGCAGATATCAATGGCAAACAGTTCCTTGTCACTAGGGGTTGGATGTTGGCTGCTATTGGGTCTCT
TGGAGCATAGAGCACAAGCTGGCCCACTGGGTCGCCTATGTAGTGAAATTATTTGATGAAGAATCATATAGCATCTTGCA
AAAGGCTCAGTGTAACAATGAGGACACCTCTGATATCAAATCCCTCTTTACAGTCAGTATGGACCATCTAGGTGCCTGGA
GAGGACCATGTGTTTCTACTAAGGTGTTGGCGGCTTCATTGGTCTCCTAGTATGTTATATGGCTTTCAGTGTCGAGAGTA
ATATCTCAGCC

Alignment

ORF - retro_acar_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 64.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVALYADVNGKQFPVTRGQ-DVGRYQVSWSMEHKLARSGTYEVKFFDEESYSILRKAQRNNEDVSDIKPL
          ..ALYAD.NGKQF.VTRG..DVG.Y.VSWS.EHKLA....Y.VK.FDEESYSIL.KAQ.NNED.SDIK.L
Retrocopy DAALYADINGKQFLVTRGW<DVGCYWVSWSIEHKLAHWVAYVVKLFDEESYSILQKAQCNNEDTSDIKSL

Parental  FTVNVDHRGAWNGPWVSTEVLAA-LIGLLVYYMAFSAKSNIQA
          FTV..DH.GAW.GP.VST.VLAA..IGLLV.YMAFS..SNI.A
Retrocopy FTVSMDHLGAWRGPCVSTKVLAA<FIGLLVCYMAFSVESNISA

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	639.80 RPM
SRP009831_brain	0.00 RPM	73.24 RPM
SRP009831_dewlap	0.00 RPM	136.81 RPM
SRP009831_embryo	0.00 RPM	279.40 RPM
SRP009831_heart	0.00 RPM	96.97 RPM
SRP009831_liver	0.00 RPM	513.65 RPM
SRP009831_lung	0.00 RPM	207.89 RPM
SRP009831_ovary	0.00 RPM	127.21 RPM
SRP009831_skeletal_muscle	0.00 RPM	120.26 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_97 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_97 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011328	1 retrocopy	retro_acar_97 ,
Callithrix jacchus	ENSCJAG00000011167	1 retrocopy	retro_cjac_2056,
Dasypus novemcinctus	ENSDNOG00000025714	2 retrocopies	retro_dnov_1204, retro_dnov_922,
Homo sapiens	ENSG00000180879	1 retrocopy	retro_hsap_2536,
Gorilla gorilla	ENSGGOG00000024329	1 retrocopy	retro_ggor_1585,
Loxodonta africana	ENSLAFG00000006908	1 retrocopy	retro_lafr_337,
Mustela putorius furo	ENSMPUG00000008803	1 retrocopy	retro_mputfur_148,
Nomascus leucogenys	ENSNLEG00000013602	1 retrocopy	retro_nleu_2738,
Otolemur garnettii	ENSOGAG00000006738	1 retrocopy	retro_ogar_691,
Procavia capensis	ENSPCAG00000009037	1 retrocopy	retro_pcap_139,
Sus scrofa	ENSSSCG00000012784	1 retrocopy	retro_sscr_866,