RetrogeneDB ID: retro_acar_95

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:161187711..161188292(-)
• Located in intron of: ENSACAG00000011884

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUSD3
• Ensembl ID: ENSACAG00000001297
• Aliases: None
• Description: sushi domain containing 3 [Source:HGNC Symbol;Acc:28391]

Sequence

>retro_acar_95
TCCAATCCAAGAGGACAATGCAACCAGATATTGGCATCTCACCTTGACATGCCTGAGATCATCCATGGTAATGGCATCAT
TGTGGGCACAGTCATTACATTTGAGTGTTCTGCAGAACACCAACTGGTTGGACAGGGAGTCGTCACATGAATTTGGGAAG
GCAATAGCACCCAGCAGACAGCAGATATCCCTTCATGTAAATCTATATCCAAATATGAAACCTTTGGATTTAAAGTTACA
ATGATTGCCTCCATTGTGAACTGTGCAATTATTCTGCTGATGTCTATAGCTTTTTTAACCTGCTGTTTCATGTGTTAAGA
AAAGTGAGAAAAGGAGAAAGAGCTCAAAGGGATATGGAACTGTGGTACCAGCTTAAAAGTGAAGAACTGGAAAGCATGCA
AGCAGCTTATTTTGGTTATAAAGGAAGAAATAACAACAATAAACATATCAAGCATAAGGCAGCATTTGATGGTGGCTGTC
ATATGGCATATGATAACCAAGGCTTCTGCAGCTTCCATGAAGAATGCAGGAACTGAGTGTTATGGAGAAAATTATTTACA
AAGGAATTCAGCCAAAACCAT

Alignment

ORF - retro_acar_95 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.08 %
• Parental protein coverage: 70.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SNYTGQCNQIFAPHLGMSEIIHGNGTTVGTVITFRCSAEHQLVGQGVVTCIWKGNSTQWTADIPSCKPIS
          SN..GQCNQI.A.HL.M.EIIHGNG..VGTVITF.CSAEHQLVGQGVVT.IW.GNSTQ.TADIPSCK.IS
Retrocopy SNPRGQCNQILASHLDMPEIIHGNGIIVGTVITFECSAEHQLVGQGVVT*IWEGNSTQQTADIPSCKSIS

Parental  KYETFGFKIAVIASIVSCAIILLMSMAFLTCCLIKCVKK-SERRRAQR-DMQLWYQLRSEELESMQAAYF
          KYETFGFK...IASIV.CAIILLMS.AFLTCC...C..K...RR.....DM.LWYQL.SEELESMQAAYF
Retrocopy KYETFGFKVTMIASIVNCAIILLMSIAFLTCCFM-C*EK>EKRRKSSK>DMELWYQLKSEELESMQAAYF

Parental  GYKGRNNNNNKNIKNKAAFDRGSHMAYDNQGFCSFHEECNGDITGTECYGENYLQRN
          GYKGR.NNNNK.IK.KAAFD.G.HMAYDNQGFCSFHEEC...............Q..
Retrocopy GYKGR-NNNNKHIKHKAAFDGGCHMAYDNQGFCSFHEECRN*VLWRKLFTKEFSQNH

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	60.26 RPM
SRP009831_brain	0.05 RPM	3.98 RPM
SRP009831_dewlap	0.04 RPM	36.07 RPM
SRP009831_embryo	0.00 RPM	3.47 RPM
SRP009831_heart	0.00 RPM	4.20 RPM
SRP009831_liver	0.00 RPM	9.45 RPM
SRP009831_lung	0.00 RPM	2.17 RPM
SRP009831_ovary	0.00 RPM	27.37 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.47 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_95 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_95 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001297	1 retrocopy	retro_acar_95 ,
Ochotona princeps	ENSOPRG00000005344	2 retrocopies	retro_opri_234, retro_opri_581,
Rattus norvegicus	ENSRNOG00000016525	1 retrocopy	retro_rnor_1205,