RetrogeneDB ID: retro_acar_46

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343786.1:94941..97269(+)
• Located in intron of: ENSACAG00000005335

Retrocopy information

• Ensembl ID: ENSACAG00000024821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000024147
• Aliases: None
• Description: None

Sequence

>retro_acar_46
TATCCTAGATCACACACAGGGGAGAAGTTACATCAGTGTATGGAATGTGGGAAACAATTTGATTGGAAAAGTAATCTTAC
TAGACATGAAAGGACCCACACAGGGGAGAAGCCATATGAATGTGTGGAATGTGGAAAGAGCTTCAGTCAGAGTGACAAAT
TACGTTCCCATCAAAGGACCCACACAGGGGAGAAACCCTATAAATGCATAGAATGTGGAGAAAGCTTCAGTCGGAGTGAC
AGTCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATGGAATGTGGAGAAAACTTCAGTCGGAG
TGACAGTCTACGTTCCCATCAAAGGAAGCACACAGGGGAGAAGCCATATAAATGCATAGAATGTGGAGAAAGCTTCAGTC
GGAGTGACAGTCTACGTTCCCATCAAAGGAAGCACACAGGGGAGAAGCCCTATAAATGCATGGAATGTGGAGAAAACTTC
AGTCGGAGAGACAAACTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATAGAATGTGGAGAAAA
CTTCAGTCGGAGAGACAAACTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATAGAATGTGGAG
AAAGCTTCAGTCGGAGAGACAATCGACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATAGAATGT
GGAGAAAGCTTCAGTTGGAGTGACAGTCTACGTTCCCATCAACGGACCCACACAGGGGAGAAGCCATATAAATGCATAGA
ATGTGGAAAGAGTTTCAGTCAGAGTGGACATCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCACATAAATGCA
TGAAATGTGGAGAAAGCTTCAGTCAGAGTGGCAGTCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCACATAAA
TGCATAGAATGTGGAGAAAGCTTCAGTCAGAGTGGCCGTCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCACA
TAAATGCATAGAATGTGGAGAAAGCTTCAGTCGCAGTGGCAATCTACGTACCCATCAAAGGACCCACACAGGGGAGAAGC
CCTATAAATGCATGGAATGTGGGAAGAGCTTCAGTCGGAGTGACAAATTACGTTCCCATCAAAGGACCCACACAGGGGAG
AAGCCATATAAATGCATGGAATGTGGGAAGAGCTTCAGTCACAGTGATAATCTACGTTCCCATCAAAGGACCCACACAGG
GAAGAAGCCACATAAATGCATGGAATGTGGGAAGAGCTTCAGTCACAGTGATAAACTACGTTCCCATCAAAGGACCCACA
CTGGGGAGAAGCCACATAAATGCATGGAATGTGGAAAGAGCTTCAGTCGGAGTCACCATCTACGTTCCCATCAAAGGACC
CACACAGGGGAGAAGCCCTATAAATGCATGGACTGTGGAAAGAGCTTCAGTCGGAGTGACAGTCTACGTACCCATCAAAG
GACCCACACAGGGGAGAAGCCACTTAAATGCATAGAATGTGGAAAGAGCTTCAGTCGGAGTGACAGTCTACGTAGCCATC
AAAGGACGCACACAGGGGAGAAGCCACATAAATGCATAGAATGTGGAGAGAGCTTCAGTCAGAGTGACAATCTACGTTCC
CATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATGGAATGTGGAAAGAGCTTCAGTCAGAGTGACAATCTACG
TTCTCATCAAAGGACCCACACAGGGGAGAAGCCACATAAATGCGTAGAATGCGGAGAGAGCTTCAGTCAGAGTGGACATC
TACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATAGAATGTGGAGAAAGCTTCAGTCGGAGTGAC
AGTCTACGTTCCCATCAAAAGACCCACACAGGGGAGAAGCCACATAAATGCATAGAATGTGGAAAGAGTTTCAGTTGGAG
TGGACATCTACGTTCTCATCAAAGGACCCACACAGGGGAGAAGCCACATAAATGCGTAGAATGCGGAAAGAGCTTCAGTC
ACAGTGGCAATCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCATAGAATGCGGAAAGAGCTTC
AGTCGGAGTGACAGTCTACGTTCCCATCAAAGGACCCACACAGGGGAGAAGCCATATAAATGCGTAGAATGCGGAAAGAG
CTTCAGTCGGAGTGACAGTCTACGTCTCCATCAAAGGACCCACACAAGGGGAGAAGCCCATATAAAATGCATGAAATGTG
GAAGAAAG

Alignment

ORF - retro_acar_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 77.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HERTHTGEKPYKCMECGGSFSRSGSLRSHQRTHTGEKPYKCMECGGSFSRSGSLRSHQRTHTGEKPYKCM
          ..R.HTGEK...CMECG..F.....L..H.RTHTGEKPY.C.ECG.SFS.S..LRSHQRTHTGEKPYKC.
Retrocopy YPRSHTGEKLHQCMECGKQFDWKSNLTRHERTHTGEKPYECVECGKSFSQSDKLRSHQRTHTGEKPYKCI

Parental  ECGGSFSRSGSLRSHQRTHTGEKPYKCMECGKSFSQSCHLRSHQMTHTGEKPYKCMECGKSFSQSCHLHS
          ECG.SFSRS.SLRSHQRTHTGEKPYKCMECG..FS.S..LRSHQ..HTGEKPYKC.ECG.SFS.S..L.S
Retrocopy ECGESFSRSDSLRSHQRTHTGEKPYKCMECGENFSRSDSLRSHQRKHTGEKPYKCIECGESFSRSDSLRS

Parental  HQRTHTGEKPYKCMECGESFSQSGHLRFHQRTHTGEKPLKCVECGKSFSHSSHLRTHQRTHTGEKPYKCI
          HQR.HTGEKPYKCMECGE.FS....LR.HQRTHTGEKP.KC.ECG..FS....LR.HQRTHTGEKPYKCI
Retrocopy HQRKHTGEKPYKCMECGENFSRRDKLRSHQRTHTGEKPYKCIECGENFSRRDKLRSHQRTHTGEKPYKCI

Parental  ECGVSFSHRGSLRYHQRTHTGEKPYKCIECGKSFSWKHSLTVHERTHTGEKPYKCIECGESFSWNGSLRS
          ECG.SFS.R...R.HQRTHTGEKPYKCIECG.SFSW..SL..H.RTHTGEKPYKCIECG.SFS..G.LRS
Retrocopy ECGESFSRRDNRRSHQRTHTGEKPYKCIECGESFSWSDSLRSHQRTHTGEKPYKCIECGKSFSQSGHLRS

Parental  HQRTHTGEKPYKCMKCGESFSQSGSLRSHQRTHTGEKPYKCMECGESFSQSGSLRSHQRTHTGEKPYKCM
          HQRTHTGEKP.KCMKCGESFSQSGSLRSHQRTHTGEKP.KC.ECGESFSQSG.LRSHQRTHTGEKP.KC.
Retrocopy HQRTHTGEKPHKCMKCGESFSQSGSLRSHQRTHTGEKPHKCIECGESFSQSGRLRSHQRTHTGEKPHKCI

Parental  ECGKNFSRSGSLRSHQRTHTGEKPYKCIECGESFIQSDHLRSHQRTHTGEKPYKCIECGESFSRSGSLRS
          ECG..FSRSG.LR.HQRTHTGEKPYKC.ECG.SF..SD.LRSHQRTHTGEKPYKC.ECG.SFS.S..LRS
Retrocopy ECGESFSRSGNLRTHQRTHTGEKPYKCMECGKSFSRSDKLRSHQRTHTGEKPYKCMECGKSFSHSDNLRS

Parental  HRRTHTREKPYKCMECGENFSWSSSLHSHQRTHTGEKPYKCIECGESFSRSDSLRSHQRTHTGEKPHKCM
          H.RTHT..KP.KCMECG..FS.S..L.SHQRTHTGEKP.KC.ECG.SFSRS..LRSHQRTHTGEKP.KCM
Retrocopy HQRTHTGKKPHKCMECGKSFSHSDKLRSHQRTHTGEKPHKCMECGKSFSRSHHLRSHQRTHTGEKPYKCM

Parental  ECGENFSWSSSLRSHQRTHTGEKPHKCMECGKSFNQSGNLRSHQRTHTGEKPHKCMECGKSFRQSCNLRT
          .CG..FS.S.SLR.HQRTHTGEKP.KC.ECGKSF..S..LRSHQRTHTGEKPHKC.ECG.SF.QS.NLR.
Retrocopy DCGKSFSRSDSLRTHQRTHTGEKPLKCIECGKSFSRSDSLRSHQRTHTGEKPHKCIECGESFSQSDNLRS

Parental  HQRKHTGEKPYKCMECGKSFSQKHSLTVHERTHTGEKPYKCIECGESFSWNGSLRSHQRTHTGEKPYKCM
          HQR.HTGEKPYKCMECGKSFSQ...L..H.RTHTGEKP.KC.ECGESFS..G.LRSHQRTHTGEKPYKC.
Retrocopy HQRTHTGEKPYKCMECGKSFSQSDNLRSHQRTHTGEKPHKCVECGESFSQSGHLRSHQRTHTGEKPYKCI

Parental  KCGESFSQSGSLRSHQRTHTGEKPYKCMECGESFSQSGSLRSHQRTHTGEKPYKCMECGKNFSRSGSLRS
          .CGESFS.S.SLRSHQ.THTGEKP.KC.ECG.SFS.SG.LRSHQRTHTGEKP.KC.ECGK.FS.SG.LRS
Retrocopy ECGESFSRSDSLRSHQKTHTGEKPHKCIECGKSFSWSGHLRSHQRTHTGEKPHKCVECGKSFSHSGNLRS

Parental  HQRTHTGEKPYKCIECGESFIQSDHLRSHQRTHTGEKPHKCIECGESFSRSDSLRSHKRTHT-GEKPYKC
          HQRTHTGEKPYKCIECG.SF..SD.LRSHQRTHTGEKP.KC.ECG.SFSRSDSLR.H.RTHT.GE...KC
Retrocopy HQRTHTGEKPYKCIECGKSFSRSDSLRSHQRTHTGEKPYKCVECGKSFSRSDSLRLHQRTHTRGEAHIKC

Parental  IECG
          ..CG
Retrocopy MKCG

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	1.48 RPM	0.33 RPM
SRP009831_brain	0.80 RPM	0.28 RPM
SRP009831_dewlap	1.14 RPM	7.72 RPM
SRP009831_embryo	1.39 RPM	1.84 RPM
SRP009831_heart	1.92 RPM	1.35 RPM
SRP009831_liver	0.41 RPM	0.12 RPM
SRP009831_lung	3.22 RPM	1.21 RPM
SRP009831_ovary	2.51 RPM	11.43 RPM
SRP009831_skeletal_muscle	1.06 RPM	0.62 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_46 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_46 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000022348	1 retrocopy	retro_acar_50,
Anolis carolinensis	ENSACAG00000024100	1 retrocopy	retro_acar_28,
Anolis carolinensis	ENSACAG00000024147	1 retrocopy	retro_acar_46 ,
Danio rerio	ENSDARG00000089344	1 retrocopy	retro_drer_10,
Xenopus tropicalis	ENSXETG00000024377	1 retrocopy	retro_xtro_31,