RetrogeneDB ID: retro_acar_28

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344817.1:7664..9254(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000000122
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000024100
• Aliases: None
• Description: None

Sequence

>retro_acar_28
TGTGGAAAGAGCTTTAGTCAGCATGGAAAGCTGAAGAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCT
GGAGTGTGGACAGAGCTTCACTCATAGTTCAGGTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTTTAAAT
GCCTGGAGTGTGAACAGAGCTTCACTCGGAGTTCAGGTCTACGTTCGCATCAAAGGACTCACACTGGGGAGAAACCCTAT
AAATGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAGGTCTACGTAGACATCAAAGGACTCACACTGGGGAGAAACC
CTTTAAATGCCTGGAGTGTGGACAGAGCTTCACTCGGAGTTCAGGTCTACGTTCACATCAAAGGACTCACACTGGGGAGA
AACCCTTTAAATGCCTGGAGTGTGAACAGAGCTTCACTCGGAGTTCAGGTCTACGTTCGCATCAAAGGACTCACACTGGG
GAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCATAGTTCAGGTCTACGTAGACATCAAAGGACTCACAC
TGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTTGCTCGTAGTTCAGGCCTACATTCACATCAAAGGATTC
ACACTGGGGAGAAACCCTTTAAATGCCTGGAGTGTGGACAGAGCTTCACTCATAGCTCAGGCCTACGTAGACATCAAAGG
ACTCACACTGGGGAGAAACCCTTTAAATGCCTGGAGCGTGAACAGAGCTTCATTCAGAGTTCAGTTCTACGTAGACATCA
AAGGACTCACACTAGGGAGAAACCCTTTAAATGCCTGGAGTGTGGACAGAGCTTCACTCGTAGCTCAGGCCTACGTAGAC
ATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTTGTAATGGAAGTCTACAT
TTACATCAAAGGACTCACACTGGGGAGAAACCCTTTAAATGCCTGGAGTGTGGACAGAGCTTCACTCAAAGCTCAGGCCT
ACGTAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAAGGCTTTGCTGATAGTTCAG
GCCTACATTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCATGTATAGT
TCACATCTACGTAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCG
TAGTTCAGGTTTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCA
CTCATAGTTCAGGCTTACGTAGACATCAAAGGACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGC
TTCACTCGTAGTTCAAGCCTACGTTCCCATCAAAGGACTCACACTGGGGAGAAACCTTATAAATGCCTGGAGTGTGGACA
GAGCTTCACTCGTAGTTCAGGCCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATACATGC

Alignment

ORF - retro_acar_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 58.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CEQSFTQSSGLHSHQRTHTGEKPFKCLECGQSFAHNGSLHSHQRTHTGEKPYKCVECGQSFTQNSGLRTH
          C..SF.Q...L..HQRTHTGEKP..CLECGQSF.H...L.SHQRTHTGEKP.KC.EC.QSFT..SGLR.H
Retrocopy CGKSFSQHGKLKRHQRTHTGEKPYNCLECGQSFTHSSGLRSHQRTHTGEKPFKCLECEQSFTRSSGLRSH

Parental  QRTHTGEKPYNCLQCGQSFTHRSGLRRHQRIHTGEKPYTCLECGQSFSRSSGLRSHQRTHTGEKPFKCLE
          QRTHTGEKPY.CL.CGQSFTH.SGLRRHQR.HTGEKP..CLECGQSF.RSSGLRSHQRTHTGEKPFKCLE
Retrocopy QRTHTGEKPYKCLECGQSFTHSSGLRRHQRTHTGEKPFKCLECGQSFTRSSGLRSHQRTHTGEKPFKCLE

Parental  CEQSFTHRSGLRRHQRIHTGEKPYTCLECGQSFTHSSGLRSHQRIHTGEKQYKCLECGQSFTHSSGLRSH
          CEQSFT..SGLR.HQR.HTGEKPY.CLECGQSFTHSSGLR.HQR.HTGEK.YKCLECGQSF..SSGL.SH
Retrocopy CEQSFTRSSGLRSHQRTHTGEKPYKCLECGQSFTHSSGLRRHQRTHTGEKPYKCLECGQSFARSSGLHSH

Parental  QRTHTGEKQYKCLECGQSFTHSSGLRSHQRTHTGEKPYKCLECGQSFAQSGTLHSHQRSHTGEKPYKCLE
          QR.HTGEK..KCLECGQSFTHSSGLR.HQRTHTGEKP.KCLE..QSF.QS..L..HQR.HT.EKP.KCLE
Retrocopy QRIHTGEKPFKCLECGQSFTHSSGLRRHQRTHTGEKPFKCLEREQSFIQSSVLRRHQRTHTREKPFKCLE

Parental  CGQSFTHSSGLRRHQRTHTGEKPYKCLECVFVFGYNSGLRTHQRTHTGEKPFECLECGQSFTHSSGLRSH
          CGQSFT.SSGLRRHQRTHTGEKPY.CLEC...F..N..L..HQRTHTGEKPF.CLECGQSFT.SSGLR.H
Retrocopy CGQSFTRSSGLRRHQRTHTGEKPYNCLECGQSFACNGSLHLHQRTHTGEKPFKCLECGQSFTQSSGLRRH

Parental  QRTHTGEKPYKCLECGQSFTHSSVLRSHQRTHTGEKPYKCLECGQSFTQKGHLHSHQRTHTGEKPYKCLE
          QRTHTGEKPYKCLECGQ.F..SS.L.SHQRTHTGEKPYKCLECGQSF....HL..HQRTHTGEKPYKCLE
Retrocopy QRTHTGEKPYKCLECGQGFADSSGLHSHQRTHTGEKPYKCLECGQSFMYSSHLRRHQRTHTGEKPYKCLE

Parental  CGQSFTQNSGLRTHQRTHTGEEPYTCLECGQSFTQNSGLCRHQRTHTGEKPYKCLECGQSLTRSSGLRSH
          CGQSFT..SGLR.HQRTHTGE.PY.CLECGQSFT..SGL.RHQRTHTGEKPY.CLECGQS.TRSS.LRSH
Retrocopy CGQSFTRSSGLRSHQRTHTGEKPYKCLECGQSFTHSSGLRRHQRTHTGEKPYTCLECGQSFTRSSSLRSH

Parental  QRTHTGEKPYKCLECGQSFTRGSGLRSHQRTHTGEKPYKC
          QRTHTGEKPYKCLECGQSFTR.SGLRSHQRTHTGEKPY.C
Retrocopy QRTHTGEKPYKCLECGQSFTRSSGLRSHQRTHTGEKPYTC

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	0.13 RPM	5.19 RPM
SRP009831_brain	0.71 RPM	3.69 RPM
SRP009831_dewlap	0.38 RPM	12.07 RPM
SRP009831_embryo	2.10 RPM	5.63 RPM
SRP009831_heart	0.42 RPM	5.03 RPM
SRP009831_liver	0.00 RPM	1.06 RPM
SRP009831_lung	0.00 RPM	2.62 RPM
SRP009831_ovary	0.42 RPM	14.13 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.76 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_28 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_28 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,