RetrogeneDB ID: retro_acar_23

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343571.1:296401..298267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000022711
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000026721
• Aliases: None
• Description: None

Sequence

>retro_acar_23
ATGGAGAAGAAACCCGATAAATGCCTGGACTATGGACAGAACTTCGCTGAGAGTGGAAATCTACAATCACACCAAGGGAC
ACACACTGGGGAGAAACCCTATAAATGTCTGACATGTGGACAGAGCTTCACTAGGAATGAAAATTTACGTTCACATCAAA
GGACTCACACTGGGGAGAAACCCTTTATGTGCCTGACGTGTGGACGGGGCTTCGCTCAAAGTTCAAGTTTACGTTCACAT
CAAAGGACTCACACTGGGGAGAAACCCTATGTATGCCAGGAGTGTGGACACAGCTTTAGTAAGAGTTCAAGTCTACGTTC
ACATCAATGGACTCACACTGAAGAGAAACCCTATAAATGCCTTGTGTGTGGACACAGTTTTACTAGGAGTGAACATCTAT
CTTCACATCAAAGGACTCACACTGGGGAGAAACCCTTTACGTGCCTGACATGTGGGCAGAGCTTCGCTCATAGTTCAAGT
CTATCCTCACATCAAAGGACTCACACTGGGGAGAAACCCTATATATGCCTGGAGTGTGGACAGAGCTTTACTAAGAGTGA
CCATCTATGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTTTATGTGCCTGACGTGTGGACAGAGCTTTGCTCAAA
CTTCAAGTCTACGTTCACATCAGAGGACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGCTTCACT
CAGAGTTCAGATCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGCTT
CACTCAGAGTTCAGATCTACGTTCACATCAAGGGACTCACACTGGGGAGAAACCCTATAAATGCCAGGAATGTGGACAGA
GCTTCACTCACAGAGCAACTCTACGTTCGCATCTAAGGACTCACACTGGGGAAAAACCCTATAAATGCAAGGAATGTGGA
CAGAGCTTCACTATGAGTGGACATCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATGAATGCCAGGAGTG
TGGACAGAGTTTCACTCAGTTGGGACATCTACAAAGACATCAAAGGATTCACACTGGAGAGAAACCATATAAATGCCTGG
AGTGTGGACAGAATTTCACTCAGAGGGAACATCTACGTTTGCATCAAAGGACTCACACTGGGGAGAGACCCTATAAATGC
CTGGAATGTGGACAGAGCTTCACTCAAAGTTCAAATCTACATAAGCATCAAAGGACTCACACTGGGGAGAAACCCTATAA
ATGCCTGGAGTGTGGACAGAGCTTCACTCAAAGTTCAAATCTACTTTCACATCAGGGAACTCACACTGGGGAGAAACCCT
ATATCTGCCTCGAATGTGGACACGGCTTTGCTAACAGTGAACATCTATGTTCACATCAAAGGACTCACACTGGGGAGAAA
CCCTATAATTGCCTGGATTGTGGAAAGAGCTTCACTAGCAGTGGTAATCTACAGTCACATCAAAGGACTCACACTGGGGA
GAAACCCTATAATTGCCTGGAGTGTGGAAAGAGCTTCACTAGCAGTGGACATCTACATTCACATCAGAGGACTCACACTG
GGGAGAAACCTTACAAATGCCTGGAGTGTGGAAAGAGCTTCACTAGCAGTGGAAATCTACTTTCACATCAAAGGACTCAC
ACTGGGGAGAAACCCTATGAATGCCTGGAGTGTGGAAAGAGCTTCTCTAGGAGTGGAAATCTGCTTTCACATCAAAGGAC
TCACACTGGGGAGAAACCCTATACATGCCTAGAATGTGGACGTAGTTTCACTGAGAGTGGACATCTACGTTTGCATCAAA
GGACTCACACTGGGGAGAAACCCTAG

Alignment

ORF - retro_acar_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.67 %
• Parental protein coverage: 78.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPYKCLECGQSFTRKGSLQTHQRTHTGEKPYKCLECEQSFTRSSALRIHQWTHTGEKPFKCLECEQSFT
          .KP.KCL..GQ.F...G.LQ.HQ.THTGEKPYKCL.C.QSFTR...LR.HQ.THTGEKPF.CL.C...F.
Retrocopy KKPDKCLDYGQNFAESGNLQSHQGTHTGEKPYKCLTCGQSFTRNENLRSHQRTHTGEKPFMCLTCGRGFA

Parental  RSSALRIHQWTHTGEKPFKCLECEQRFTRSSDLHSHQRTHTGEKPYKCLECGQSFAHSSGLRSHQRTHTG
          .SS.LR.HQ.THTGEKP..C.EC...F..SS.L.SHQ.THT.EKPYKCL.CG.SF..S..L.SHQRTHTG
Retrocopy QSSSLRSHQRTHTGEKPYVCQECGHSFSKSSSLRSHQWTHTEEKPYKCLVCGHSFTRSEHLSSHQRTHTG

Parental  EKPYKCLECEQSFSRSSALRIHQWTHTGEKPFKCLECEQSFTRSSDLHSHQRTHTGEKPYKCLECGQSFA
          EKP..CL.C.QSF..SS.L..HQ.THTGEKP..CLEC.QSFT.S..L.SHQRTHTGEKP..CL.CGQSFA
Retrocopy EKPFTCLTCGQSFAHSSSLSSHQRTHTGEKPYICLECGQSFTKSDHLCSHQRTHTGEKPFMCLTCGQSFA

Parental  HSSGLRSHQRTHTGEKPYKCLECEQSFTQKGSLHRHQRTHTGEKPYKCLECGQSFTQSSHLHRHQRTHTG
          ..S.LRSHQRTHTGEKPY.CLEC.QSFTQ...L..HQRTHTGEKPY.CLECGQSFTQSS.L..HQ.THTG
Retrocopy QTSSLRSHQRTHTGEKPYTCLECGQSFTQSSDLRSHQRTHTGEKPYTCLECGQSFTQSSDLRSHQGTHTG

Parental  EKPYKCLECGQSFAHSSGLRSHQRTHTGEKPYKCLECGQSFSHNSHLHRHQRTHTGEKPYNCLECGQSFT
          EKPYKC.ECGQSF.H...LRSH.RTHTGEKPYKC.ECGQSF....HL..HQRTHTGEKPY.C.ECGQSFT
Retrocopy EKPYKCQECGQSFTHRATLRSHLRTHTGEKPYKCKECGQSFTMSGHLRSHQRTHTGEKPYECQECGQSFT

Parental  EKGSLHKHQRTHTGEKPYKCLECGQSFTQSSGLRRHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTG
          ..G.L..HQR.HTGEKPYKCLECGQ.FTQ...LR.HQRTHTGE.PY.CLECGQSF..SS.L..HQRTHTG
Retrocopy QLGHLQRHQRIHTGEKPYKCLECGQNFTQREHLRLHQRTHTGERPYKCLECGQSFTQSSNLHKHQRTHTG

Parental  EKPYNCLECGQSFARSSGLRSHQRTHTGEKPYNCLECGQSFARSSGLCSHQRTHTGEKPYNCLECGQSFI
          EKPY.CLECGQSF..SS.L.SHQ.THTGEKPY.CLECG..FA.S..LCSHQRTHTGEKPYNCL.CG.SF.
Retrocopy EKPYKCLECGQSFTQSSNLLSHQGTHTGEKPYICLECGHGFANSEHLCSHQRTHTGEKPYNCLDCGKSFT

Parental  DCSTLRSHQRTHTGEKPYKCLECGQSFARSSALRSHQRTHTEEKPYKCLECGQSFTQRGHLRSHQRTHTG
          ....L.SHQRTHTGEKPY.CLECG.SF..S..L.SHQRTHT.EKPYKCLECG.SFT..G.L.SHQRTHTG
Retrocopy SSGNLQSHQRTHTGEKPYNCLECGKSFTSSGHLHSHQRTHTGEKPYKCLECGKSFTSSGNLLSHQRTHTG

Parental  EKPYNCLECGQSFAVSSGLRSHQKTHTGEKPCKCLECGQSFTQGGHLRSHERTHTGEKP
          EKPY.CLECG.SF..S..L.SHQ.THTGEKP..CLECG.SFT..GHLR.H.RTHTGEKP
Retrocopy EKPYECLECGKSFSRSGNLLSHQRTHTGEKPYTCLECGRSFTESGHLRLHQRTHTGEKP

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	4.43 RPM	11.09 RPM
SRP009831_brain	2.65 RPM	0.52 RPM
SRP009831_dewlap	12.74 RPM	1.48 RPM
SRP009831_embryo	9.93 RPM	8.24 RPM
SRP009831_heart	3.84 RPM	12.24 RPM
SRP009831_liver	1.55 RPM	3.11 RPM
SRP009831_lung	2.42 RPM	7.30 RPM
SRP009831_ovary	10.08 RPM	3.44 RPM
SRP009831_skeletal_muscle	1.42 RPM	1.68 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_23 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_23 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,