RetrogeneDB ID: retro_acar_148

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 6:67068949..67069564(-)
• Located in intron of: ENSACAG00000017346

Retrocopy information

• Ensembl ID: ENSACAG00000017358
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PARP16
• Ensembl ID: ENSACAG00000004437
• Aliases: None
• Description: None

Sequence

>retro_acar_148
AGCGTGCTGGTGGCTGAGCCAGACTTCCTGTTTGAGATCACCTATTCCAGCCAGATGAATGCCAAATTCAATGAGACCAA
AGCGGGGAGAGATCTCTATTCTTTTCATGGGAGCCGCCTCAAGAACTTCCACTCCATCGTCCACAATGGGCTGCAATGCC
ACCTGAACTGGACCTCCTTGTTCGGGGAAGATACCTACCTGACCAGTGACTTGAGTCTTGCTCTCCTCTATAGCCCCCAC
GGACTCGGCTGGCAGTGGTGCCTCATGGGCTCCGTCCTGAGCTGCATCGCCGTTTGCAAAATCATAGATCACCTGGATGT
CAAGTGCCCAGACCAAAAGAAAGATTCTAAAGAAATCAACAAGACTAGAGCCAGAGTGAAGAACAGCGAAGACAGCAATG
TCCCTCGGAAATACTCTCTGGTAACAAACAACCAGCTGATCCAAGTGAAGTACTTGCTGGTATATTTGGAGAAGCAATAT
CGCAGGTGTTCCAACCAGTTGTGGCTCTCCTTCGCACTGCTTTGCCTTGATGATGAGCCTCTCCCATCTGCTCCTGATGC
TCATTGGCACCAGCAACTCCCCAGCTTTCCTGTCCTATTGAGCAGACTCTTTGAT

Alignment

ORF - retro_acar_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVPVAEPDFLFEITYSSQMNAKFEETKAGRDLLYAFHGSRLENFHSIVHNGLQCHLNRTSLFGEGTYLTS
          SV.VAEPDFLFEITYSSQMNAKF.ETKAGRDL.Y.FHGSRL.NFHSIVHNGLQCHLN.TSLFGE.TYLTS
Retrocopy SVLVAEPDFLFEITYSSQMNAKFNETKAGRDL-YSFHGSRLKNFHSIVHNGLQCHLNWTSLFGEDTYLTS

Parental  DLSLALLYSPHGLGWQRSLMGPVLSCVAVCEIIDHPDVKCQVQKKVDSKEIDKKRARVRNSEGGDVPPMY
          DLSLALLYSPHGLGWQ..LMG.VLSC.AVC.IIDH.DVKC..QKK.DSKEI.K.RARV.NSE...VP..Y
Retrocopy DLSLALLYSPHGLGWQWCLMGSVLSCIAVCKIIDHLDVKCPDQKK-DSKEINKTRARVKNSEDSNVPRKY

Parental  FLDEDYKLVQDVDLLRHCLPLPFRCSSQSWLS-SHRFALMMSLYLLLLMLIGASNSPAFLSY-WSRLFD
          .L.....L.Q...LL........RCS.Q.WLS.SH.FALMMSL..LLLMLIG.SNSPAFLSY..SRLFD
Retrocopy SLVTNNQLIQVKYLLVYLEKQYRRCSNQLWLS>SHCFALMMSLSHLLLMLIGTSNSPAFLSY<LSRLFD

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	0.10 RPM	9.12 RPM
SRP009831_brain	0.09 RPM	5.07 RPM
SRP009831_dewlap	0.00 RPM	21.94 RPM
SRP009831_embryo	0.06 RPM	21.46 RPM
SRP009831_heart	0.10 RPM	12.40 RPM
SRP009831_liver	0.00 RPM	8.59 RPM
SRP009831_lung	0.45 RPM	8.76 RPM
SRP009831_ovary	0.00 RPM	29.42 RPM
SRP009831_skeletal_muscle	0.00 RPM	2.51 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_148 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_148 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004437	1 retrocopy	retro_acar_148 ,
Macropus eugenii	ENSMEUG00000001881	1 retrocopy	retro_meug_672,