RetrogeneDB ID: retro_acar_73

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:229491798..229492485(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000028325
• Aliases: None
• Description: None

Sequence

>retro_acar_73
AGTCCACCCCAGTGCTGCTCCCTTTTACCAGGGAAGAGGGGCTGGAGCCATAGCCATGCCTCCGGATGGCAACGAGACAT
GATACTCAAAGGGACATGGTTCAGGACAAGCCAAGGAGTGGTGAACTTCAGTGGTACACATTGAACCCGGTGCCGCCCAT
GACCTCTGACTTTTAAACACCATTTGGAGCAGAGAGATCAGGAGACCAATTCCAAGCACTTTGTCTCAGAGGACAAGATG
GTTGCTCACTTTAACTCCCTTAGCTTGGAAAACAACCACATCTACAGCTCTAATGGCTTCCCTATCCACAACAAAGATCC
CCAATGGCAGCAAGCCTAGTCATGCCTGAAAGAGCTACAACAAAGGCTCTCCCAAGACAGAACGCAAAAAGAAACCTGCT
CAGATGATTAAGATGCACTCAACAACGTTATTGTGAACAGAGAATACATCATGGGCTAGTGCCCTTGCTGACGTACCCTT
CTCTCTTATGAGCCAGACTTGAAAACGTTGTGATTACACCTGAAGAACTGCTTCTCTCTTTGAATCCTTGTACAGAGGAT
CTCATGGAGCCCTCACAATAAGTCAAGCTTACACACCATTCGGACAATGATGGGTATCCCCTCTTCCTTGAGTGCCTCTG
TAGAGGCCCAGAAAAAAGTGGTGGGAACAGAAGAGGAAATGGAAGTA

Alignment

ORF - retro_acar_73 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 93.88 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPSQRCSLLPGKRGWSHSHVSGWQRDMTRKGTWFRTSQGVVNFSGTQRSRCRPGPLTFKRHLEHRDQEPN
          SP.Q.CSLLPGKRGWSHSH.SGWQRDM..KGTWFRTSQGVVNFSGT...RCRP.PLTFK.HLE.RDQE.N
Retrocopy SPPQCCSLLPGKRGWSHSHASGWQRDMILKGTWFRTSQGVVNFSGTH*TRCRP*PLTFKHHLEQRDQETN

Parental  SKHFLSEDKMAARFNSLSLENDHIYSSNGFPIHDEDPQWQQAYSRLKELQQRLSQDRAQDETCSDDEDEL
          SKHF.SEDKM.A.FNSLSLEN.HIYSSNGFPIH..DPQWQQA.S.LKELQQRLSQDR.Q.ETCSDD.D.L
Retrocopy SKHFVSEDKMVAHFNSLSLENNHIYSSNGFPIHNKDPQWQQA*SCLKELQQRLSQDRTQKETCSDD*DAL

Parental  NNVIVDGEYIMGECP-LLTHPSLLRAGLGEVGITAEELLL-SLNPCTEVVLWSPHNKTSLHTIRTMMGIP
          NNVIV..EYIMG.CP.LLT.PSLL.A.L..V.IT..E.LL.SL........WSPHNK.SLHTIRTMMGIP
Retrocopy NNVIVNREYIMG*CP<LLTYPSLL*ARLENVVITP-EELL>SL*ILVQRISWSPHNKSSLHTIRTMMGIP

Parental  SSASTSVEAQQKAAGAEEEMEV
          SS.S.SVEAQ.K..G.EEEMEV
Retrocopy SSLSASVEAQKKVVGTEEEMEV

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	14.93 RPM
SRP009831_brain	0.05 RPM	15.53 RPM
SRP009831_dewlap	0.00 RPM	34.26 RPM
SRP009831_embryo	0.03 RPM	5.72 RPM
SRP009831_heart	0.05 RPM	13.23 RPM
SRP009831_liver	0.00 RPM	8.47 RPM
SRP009831_lung	0.20 RPM	18.59 RPM
SRP009831_ovary	0.00 RPM	32.89 RPM
SRP009831_skeletal_muscle	0.00 RPM	6.45 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_73 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_73 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028325	1 retrocopy	retro_acar_73 ,