RetrogeneDB ID: retro_acar_51

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344068.1:52532..54230(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000026313
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000008838
• Aliases: None
• Description: None

Sequence

>retro_acar_51
ATGGAGGAGAAAGCATATAAATGTATCGAATGTGGAAAGAGCTTTAGTAAGCATGGAAACATGAAGAGACATCAAAGGAT
TCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCAGAAGGGAAGCTTACATACACATCAAA
GGACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAACTTCACCCATAGTTCAGGCCTACGTTCACAT
CAAAGGATTCACACTGGGGAGAAACCCTACAACTGCCTAGAGTGTGGACAGAGCTTTGCTCAGAAGGGAAGCTTACATAC
ACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAGGCCTAC
GCAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAAAGCTTCACTCGTAGTTCAGGC
CTACGTAGACATCAAAGGACTCACACTGTGGATAAACCCTATAACTGCCTGAAGTGTGGACAGAGCTTTACTCAGAAGGG
ACAATTACATTCACATCAAAGGACTCACAGTGGGGAGAAACCCTATAATTGCCTTGAGTGCGGACAGAGCTTCATTCATA
GTTCAGGCCTACGCAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGACCTTTGCT
CAGAAGGGACACTTACATTCACATAAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTT
TGCTCAGAAGGGACACTTACATTCACATGAAAGGACTCACACTGGGGAGAAACCCTATATATGCCTTGAGTGTGGACAGA
GCTTCACTCATAGGTCAAATCTACACTCACATCAAAGGACTCACACTGGGGAGAAACCTTATAAATGCCTGGAGTGTGGA
CAGAGCTTTACTCAGCAGGGGCACTTACATTCACATCAAAGGACTCACACGGGGGAGAAACACTATAACTGCCTGGAGTG
TGGACAGAGCTTTGCTCGTAGTTCAGGAATACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGG
AGTGTGAACAGAGCTTTGCTTGTAGTTCAGGACTGCGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGC
CTGGAGTGTGGGCAGAGCTTCACTCATAGTTCAGCACTATGTAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAA
CTGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAGCACTACGTAGACATCAAAGGACTCACACTGGGGAGAAACCCT
ATAACTGCCTGGAGTGTGGACAGAGCTTTACTCATAGATCAGGCCTACGATCACATGAAAGGACTCACACTGGAGAGAAA
CCGTATAACTGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAAGCTTACGTAGACATCAAAGGACTCACACTGGGGA
GAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAGGTCTACGTTCACATCAACGGACTTACACTG
GGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTTGCTCAGAGTGGAAATTTACGTTCACATCAAAGGACTCAG
ACTGGGGAGAAACCATAG

Alignment

ORF - retro_acar_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.5 %
• Parental protein coverage: 72.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPYNCLECGQSFTRKGHLHSHQRTHTGEKPYNCLECGQSFTQKGSLHSHQRIHTGEKPYTCLKCGQNFT
          EK.Y.C.ECG.SF...G....HQR.HTGEKPYNCLECGQSF.QKGSLH.HQR.HTGEKPYTCL.CGQNFT
Retrocopy EKAYKCIECGKSFSKHGNMKRHQRIHTGEKPYNCLECGQSFAQKGSLHTHQRTHTGEKPYTCLECGQNFT

Parental  YSSGLRSHQRIHTGEKPYNCLECGQSFAQKGSLHTHQRTHTGEKPYNCLECGQSFARSSGLRSHQRTHTG
          .SSGLRSHQRIHTGEKPYNCLECGQSFAQKGSLHTHQRTHTGEKPY.CLECGQSF..SSGLR.HQRTHTG
Retrocopy HSSGLRSHQRIHTGEKPYNCLECGQSFAQKGSLHTHQRTHTGEKPYKCLECGQSFTHSSGLRRHQRTHTG

Parental  EKPYKCLECGQSFTRSSGLRSHQRTHTGEKPYNCLECGQSFTHSSALCRHQRTHTGEKPYNCLECGQSFT
          EKPYKCLECGQSFTRSSGLR.HQRTHT..KPYNCL.CGQSFT....L..HQRTH.GEKPYNCLECGQSF.
Retrocopy EKPYKCLECGQSFTRSSGLRRHQRTHTVDKPYNCLKCGQSFTQKGQLHSHQRTHSGEKPYNCLECGQSFI

Parental  HRSGLRSHERTHTGEKPYKCLECGQSFTHSSGLRSHQRTHTGEKPYNCLECGQSFTHSSSLRRHQRTHTG
          H.SGLR.H.RTHTGEKPY.CLECGQ.F.....L.SH.RTHTGEKPYNCLECGQSF.....L..H.RTHTG
Retrocopy HSSGLRRHQRTHTGEKPYNCLECGQTFAQKGHLHSHKRTHTGEKPYNCLECGQSFAQKGHLHSHERTHTG

Parental  GKPYKCLECGQSFTHSSGLHRHQRTHTGKKPYNCLECGQSFTHSNSGLRTHQRTHTGEKPYKCLECGKSF
          .KPY.CLECGQSFTH.S.LH.HQRTHTG.KPY.CLECGQSFT.....L..HQRTHTGEK.Y.CLECG.SF
Retrocopy EKPYICLECGQSFTHRSNLHSHQRTHTGEKPYKCLECGQSFTQQGH-LHSHQRTHTGEKHYNCLECGQSF

Parental  TRSSVLRSHERTHTGEKPYTCRECGKSFTRSSVLRSHERTHTGEKPYTCLECGQSFTHSSGLHSHQRTHT
          .RSS..RSH.RTHTGEKPY.C.EC..SF..SS.LRSH.RTHTGEKPY.CLECGQSFTHSS.L..HQRTHT
Retrocopy ARSSGIRSHQRTHTGEKPYNCLECEQSFACSSGLRSHQRTHTGEKPYNCLECGQSFTHSSALCRHQRTHT

Parental  GEKPYNCLECGQSFTRRSDLRSHQRTHTGEKPYTCRECGKSFTHSSGLRRHQRTHTGEKPYTCLECGQSF
          GEKPYNCLECGQSFT..S.LR.HQRTHTGEKPY.C.ECG.SFTH.SGLR.H.RTHTGEKPY.CLECGQSF
Retrocopy GEKPYNCLECGQSFTHSSALRRHQRTHTGEKPYNCLECGQSFTHRSGLRSHERTHTGEKPYNCLECGQSF

Parental  THSSGLRRHQRTHTGEKPYTCLECGQSFTQNSDLRSHQRTHTGEKPYTCLECGQSFTHSSGLRSHQWTHT
          THSS.LRRHQRTHTGEKPY.CLECGQSFT..S.LRSHQRT.TGEKPY.CLECGQSF..S..LRSHQ.T.T
Retrocopy THSSSLRRHQRTHTGEKPYKCLECGQSFTHSSGLRSHQRTYTGEKPYKCLECGQSFAQSGNLRSHQRTQT

Parental  GEKP
          GEKP
Retrocopy GEKP

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	0.30 RPM	0.85 RPM
SRP009831_brain	0.14 RPM	0.66 RPM
SRP009831_dewlap	0.55 RPM	0.84 RPM
SRP009831_embryo	1.22 RPM	2.40 RPM
SRP009831_heart	0.93 RPM	0.83 RPM
SRP009831_liver	0.16 RPM	0.25 RPM
SRP009831_lung	0.25 RPM	0.35 RPM
SRP009831_ovary	0.85 RPM	2.82 RPM
SRP009831_skeletal_muscle	0.07 RPM	0.18 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_51 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_51 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51 ,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,