RetrogeneDB ID: retro_acar_4

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: AAWZ02037391:1316..2858(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000022518
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000026389
• Aliases: None
• Description: None

Sequence

>retro_acar_4
AAGACCCATATCACTATGGACATGAAGGAGGAAACATCCAAATGTCAGGAATTTGGAAAGAGCTTCACTGAGAGTGGACA
TCTACAAAAACATGAAAGGACTCACGTTGGGGAGAGACCCTATGAATTCCTGGAGTGTGGAGAGAGCTTCACTCAGAGTG
GAAGTCTACAAAAACATGAAAGGACTCACACTGGGGAGAAACCCTATGAATTCCTGGAGTGTGGACCGAGCTTCACTCAG
AGTGGGAGTCTACAAAAACATGAAAGGACTCACACTGGGGAGAAACCCTATGAATTCCTGGAGTGTGGACCGAGCTTCAC
TCAGAGTGGGAGTCTACAAAAACATGAAAGGACTCACACTGGGGAGAAACCCTATGAATTCCTGGAGTGTGGACCGAGCT
TCACTCAGAGTGGGAGTCTACAAAAACATGAAAGGACTCACACTGGGGAGAAACCCTATGAATTCCTGGAGTGTGGACAG
AGTTTCTCTCAGAGTGGAAGTGTACATTCACATCAAAGGATTCACACTGGGGAGAAACTTTATACATGCCTGGAGTGTGG
AAAGAGCTTCGCTCTGGTTTCAAATCTGCTTTTACATCAAAGGACTCACACTGGGGAGGAACCCTATAAATGCCTGGAGT
GTGGACAGATCTTCAGTGAGAGTGGAAGTCTACGTGCACATCAGAGGACTCACACTGGGGAGAAACCTTATAAATGTATG
GAGTGTGGACAGAGCTTCACTCAGAGTTCAAGTCTATATTCACATAAAAGGATTCACACCGGGGAGAAACCCTATAAATG
CCTGGTGTGTGGACAGAGCTTCACTCAGAGTGGAAATCTACGTACACATCAAAGTACTCACACCGGGGAGAAACCCTATA
TATGCCTGGAGTGTGGACAGAGCTTCACTCAGAGTGGAAGTCTACAGAAACATAAAAGGATTCACACTGGGGAGAAACCC
TATCAATGCCTGGAGTGTGGAGAGAGCTTTGCTCTGAGTGGAAGTCTACAAAAACATAAAACGATTCACACTGGGGAGGA
ACTCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTGAGAATGGAAGTCTACAAAAACATAACAGAATTCACACTGGGG
AGAAACCTTATAAATGTCTGGAGTGTGGACAGAGCTTCGCTCAGAGTTCAAGTCTACGTTCACATCAAAGGACTCACACT
GGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCAGAGTGGACATCTACAAAAACATGAAAGGATTCA
CACTGGGGAGAGACCTTATAAATGCCTGGAGTGTGGACAGAGCTTCGCTCAGAGTGGACATCTACATAAACATGAAAGGA
TTCACACTGGGGAGAAACCCTATCAATGCCTGGAGTGTGGACAGAGCTTCACTGAGAATGGAAATCTACAAAAACATAAA
AGGATTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAAAGCTTCACTCGTAGCTCAACTCTATATTCACA
TCAAAGGACTCACTGGGGAGAA

Alignment

ORF - retro_acar_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.13 %
• Parental protein coverage: 76.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHTREKPYNCLECGQSFTQKGSLHTHRRTHTGEKPYN
          ..H......E....C.E.G.SFT..GHL..H.RTH..E.PY..LECG.SFTQ.GSL..H.RTHTGEKPY.
Retrocopy KTHITMDMKEETSKCQEFGKSFTESGHLQKHERTHVGERPYEFLECGESFTQSGSLQKHERTHTGEKPYE

Parental  CLECGQSFAHSSALYSHQRTHTGEKPYKCLDCGQSFTQKGHLHTHQRTHTGEKPYNCLECGQSFAHSSAL
          .LECG.SF..S..L..H.RTHTGEKPY..L.CG.SFTQ.G.L..H.RTHTGEKPY..LECG.SF..S..L
Retrocopy FLECGPSFTQSGSLQKHERTHTGEKPYEFLECGPSFTQSGSLQKHERTHTGEKPYEFLECGPSFTQSGSL

Parental  YSHQRTHTGEKPYKCLECGQSFTQKGHLHTHQRTHTGEKPYNCLECGQSFTQKGSLHRHQRTHTGEKPFK
          ..H.RTHTGEKPY..LECGQSF.Q.G..H.HQR.HTGEK.Y.CLECG.SF.....L..HQRTHTGE.P.K
Retrocopy QKHERTHTGEKPYEFLECGQSFSQSGSVHSHQRIHTGEKLYTCLECGKSFALVSNLLLHQRTHTGEEPYK

Parental  CLECGQSFGRSSGLRSHQRTHTGEKPYKCLECGQSFTQKKGNLHTHQRTHTGEKPYKCLECGQSFTQKGH
          CLECGQ.F..S..LR.HQRTHTGEKPYKC.ECGQSFTQ....L..H.R.HTGEKPYKCL.CGQSFTQ.G.
Retrocopy CLECGQIFSESGSLRAHQRTHTGEKPYKCMECGQSFTQSS-SLYSHKRIHTGEKPYKCLVCGQSFTQSGN

Parental  LHTHQRTHTGEKPYKCLECGQSFTQKGHLHTHQRTHTGEKPYKCLECGQSFARSSGLRSHQRTHTGEKPY
          L.THQ.THTGEKPY.CLECGQSFTQ.G.L..H.R.HTGEKPY.CLECG.SFA.S..L..H...HTGE..Y
Retrocopy LRTHQSTHTGEKPYICLECGQSFTQSGSLQKHKRIHTGEKPYQCLECGESFALSGSLQKHKTIHTGEELY

Parental  NCLECGQSFTQKGHLHTHQRTHTGEKPYKCLECGQSFAQSSGLRSHQRTHTGEKPYKCLECGQSFARSSY
          .CLECGQSFT..G.L..H.R.HTGEKPYKCLECGQSFAQSS.LRSHQRTHTGEKPYKCLECGQSF..S..
Retrocopy KCLECGQSFTENGSLQKHNRIHTGEKPYKCLECGQSFAQSSSLRSHQRTHTGEKPYKCLECGQSFTQSGH

Parental  LRKHHRIHIGEKPYKCLECGQSFTRKGSLQTHQRTHTGEKPYKCLECGQSFTCSSGLHSHQRTHTGEKPH
          L.KH.RIH.GE.PYKCLECGQSF...G.L..H.R.HTGEKPY.CLECGQSFT....L..H.R.HTGEKP.
Retrocopy LQKHERIHTGERPYKCLECGQSFAQSGHLHKHERIHTGEKPYQCLECGQSFTENGNLQKHKRIHTGEKPY

Parental  KCLECEQSFTHSSGLRRHQRTHTGE
          KCLEC.QSFT.SS.L..HQRTH.GE
Retrocopy KCLECGQSFTRSSTLYSHQRTHWGE

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	2.13 RPM	2.23 RPM
SRP009831_brain	1.61 RPM	5.02 RPM
SRP009831_dewlap	2.02 RPM	1.94 RPM
SRP009831_embryo	1.96 RPM	7.56 RPM
SRP009831_heart	1.97 RPM	5.71 RPM
SRP009831_liver	0.49 RPM	0.94 RPM
SRP009831_lung	1.36 RPM	4.33 RPM
SRP009831_ovary	1.27 RPM	1.35 RPM
SRP009831_skeletal_muscle	0.44 RPM	0.62 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_4 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_4 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,