RetrogeneDB ID: retro_acar_161

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343211.1:1034531..1034846(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAX
• Ensembl ID: ENSACAG00000017500
• Aliases: None
• Description: BCL2-associated X protein [Source:HGNC Symbol;Acc:959]

Sequence

>retro_acar_161
TATCTACCAAAGGAGGCTTTTTTCAACGTCACTGCCAGATGTTCTCTGATAGGACTTTCAACTAGGAATGAGTAGTAGTT
TTGTTCTACTTTGTGTGCAAGTTGGTCTTGAAGGCAATTTTTCACAAAAGTACCAGAGCTCATAAAGACCATCATTAGCC
ACACAATGGAGTATATCAAAAATCATATCCTGACCTAGATTCAAGCCCAGAGATGACGGGAAGGCCTCCTGTCCTACTTT
GGCACCCCAGCTTAGTAAACCATTGCTGTATTTGTGGCTGGCATCTTGACCACCTCACTGACCTTCTGGAAAATG

Alignment

ORF - retro_acar_161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YPPKEVFFRVAA-EMFSDGTFNWGRVVALFYFACKLVLKAIC-TKLPELIKTIISWTMEYIKNHVLTWIQ
          Y.PKE.FF.V.A..MFSD.TFN...VV.LFYF.CKLVLKAI..TK.PELIKTIIS.TMEYIKNH.LT.IQ
Retrocopy YLPKEAFFNVTA<QMFSDRTFN*E*VVVLFYFVCKLVLKAIF>TKVPELIKTIISHTMEYIKNHILT*IQ

Parental  AQGGWEGLLSYFGTPTWQTIAVFAAGVLTASLTFWKM
          AQ...EGLLSYFGTP...TIAVF.AG.LT.SLTFWKM
Retrocopy AQR*REGLLSYFGTPA**TIAVFVAGILTTSLTFWKM

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	7.52 RPM
SRP009831_brain	0.00 RPM	2.08 RPM
SRP009831_dewlap	0.00 RPM	3.29 RPM
SRP009831_embryo	0.00 RPM	6.49 RPM
SRP009831_heart	0.00 RPM	5.24 RPM
SRP009831_liver	0.00 RPM	2.58 RPM
SRP009831_lung	0.00 RPM	7.40 RPM
SRP009831_ovary	0.00 RPM	2.90 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.73 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_161 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_161 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017500	1 retrocopy	retro_acar_161 ,
Rattus norvegicus	ENSRNOG00000020876	2 retrocopies	retro_rnor_2592, retro_rnor_711,