RetrogeneDB ID: retro_acar_55

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:67864601..67865633(-)
• Located in intron of: ENSACAG00000011281

Retrocopy information

• Ensembl ID: ENSACAG00000011824
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000014536
• Aliases: None
• Description: None

Sequence

>retro_acar_55
CTAGCTGATACATGCATCTCTTTAGCTCTTGCTCAGCCAGCTATGAAAGCCCAACCGTTCAGAAAAACCACCAGCAGACT
TTGGTCTCTTTCAAAATTTTGTTCTTCTCTCATGAACGTGAGGGGGCAGCGCTCCTACGGCACAGAAGTAGAAAAGATTG
GCGAGCGACCTGTCCTCATCACTGGCTGTGACTCTGGGTTTGGTTTCCAGCTGGCCAAGCACCTACATGGAAAGGGTTTC
ATTGTCTATGCTGGTTGCCTACAGAAGGCGCAAGGCAAGGGAGGCTCCAAAGACCTGGATGACATGAAAAGCGATCGCAT
GAGAACCATTCAGCTCGATGTCTGTAGCAACGAAGATGTGGCGCGTGCATTGGACCATGTAACTGCCTCTCTGAAGAACC
CAGAGGCTGGACTGTGGGGTGTAGTCAACAACGCTGGGATCTCCACTTTTGGGGAGGTAGAGTTCACCAGCATGGACACC
TATAAAAAACTGGCTGAGGTGAATCTCTGGGGGACCGTCCGCACTACAAAGGCCTTCCTGCCTCTCATCCGGAGGGCCAA
GGGTCGCGTTGTGAATATAACCAGCATGCTGGGGCGGATGGCAAGCCCAGCTCGCTCCCCTTATTGCATCACCAAGTTTG
CTGTGGAAGCCTTCTCTGACTGTCTGCGCTATGAGATGCAACCCCATGAGGTCAAGGTCTGCATCGTGGAACCCGGAAAT
TTCATTGCAGGCACAAGCCTGTACAGCTCTGAAGGCATCAAGGCCACTGCCGAGAAGATGTGGAATGAGATGCCTGAAAC
AGTGCGGCAGGATTATGGACGGAAGTATTTTGATGAGCAAGTGGCCAAGATGGAGACATACTGCCAAAGTGGCTCCACAG
ACCTTTCTCCTGTCATCGAGAGCATCACTCATGCTCTGACTTCTCCCTCTCCCTATACTCGGTACCATCCCATGGACTAT
TACTGGTGGCTACGCATGCAAGTGATGACTCACTTGCCAGGTGCTATTTCGGATCGCCTGTACATTTATTAA

Alignment

ORF - retro_acar_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIGERGVLITGCDSGFGFALAKHLHERGFIIYAGCLLKEQGRGGSKELDDMKSDRMRTVQLNVCDSEEVG
          .IGER.VLITGCDSGFGF.LAKHLH..GFI.YAGCL.K.QG.GGSK.LDDMKSDRMRT.QL.VC..E.V.
Retrocopy KIGERPVLITGCDSGFGFQLAKHLHGKGFIVYAGCLQKAQGKGGSKDLDDMKSDRMRTIQLDVCSNEDVA

Parental  RAVDHVTATMKD-EAGLWGLVNNAGISTFGEVEFTSMDTYKEVAEVNLWGTIRTTKSFLPLIRRAKGRVV
          RA.DHVTA..K..EAGLWG.VNNAGISTFGEVEFTSMDTYK..AEVNLWGT.RTTK.FLPLIRRAKGRVV
Retrocopy RALDHVTASLKNPEAGLWGVVNNAGISTFGEVEFTSMDTYKKLAEVNLWGTVRTTKAFLPLIRRAKGRVV

Parental  NISSMMGRMANPARSPYCITKFGVEAFSDCLRYEMRPHDVKVCIVEPGNFIAGTSLYSPERIQAIADKMW
          NI.SM.GRMA.PARSPYCITKF.VEAFSDCLRYEM.PH.VKVCIVEPGNFIAGTSLYS.E.I.A.A.KMW
Retrocopy NITSMLGRMASPARSPYCITKFAVEAFSDCLRYEMQPHEVKVCIVEPGNFIAGTSLYSSEGIKATAEKMW

Parental  DELPEIVRRDYGRKYFDEQIAKMESYCNSGSADTSPVIDSITHALTSTTPYTRYHPMDYYWWLRMQVMTH
          .E.PE.VR.DYGRKYFDEQ.AKME.YC.SGS.D.SPVI.SITHALTS..PYTRYHPMDYYWWLRMQVMTH
Retrocopy NEMPETVRQDYGRKYFDEQVAKMETYCQSGSTDLSPVIESITHALTSPSPYTRYHPMDYYWWLRMQVMTH

Parental  MPAAISDRLYIY
          .P.AISDRLYIY
Retrocopy LPGAISDRLYIY

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	0.03 RPM	8.27 RPM
SRP009831_brain	0.05 RPM	59.70 RPM
SRP009831_dewlap	0.04 RPM	16.62 RPM
SRP009831_embryo	0.03 RPM	43.27 RPM
SRP009831_heart	0.26 RPM	92.25 RPM
SRP009831_liver	0.00 RPM	8.10 RPM
SRP009831_lung	0.00 RPM	20.35 RPM
SRP009831_ovary	0.04 RPM	26.10 RPM
SRP009831_skeletal_muscle	0.00 RPM	17.59 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_55 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_55 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	ENSACAG00000014536	1 retrocopy	retro_acar_55 ,
Latimeria chalumnae	ENSLACG00000016430	1 retrocopy	retro_lcha_85,