RetrogeneDB ID: retro_acar_13

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343710.1:193639..195505(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000024431
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_acar_13
ATGGAGGAAAAAGCATATAAATGTATTGAATGTGGAAAGAGCTTTATTCATCATGGAAACCTGAAGAGACATCAAAGGAC
TCACACTGGGGAGAAATCCTATAAATGCCTAGAGTGTGGACAGAGCTTCACTCAGAGTTCAGGTCTACGTTCACATCAAA
GGACTCACACTGGGGAGAAACCCTATAACTGTCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGACACTTACATACACAT
CAAAGAACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGAAGCTTACATAC
ACATCAAAGAACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCATAGTTCAGCACTAT
ATTCACATCAAAGGACCCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGAAGC
TTACATACGCATCAAAGAACTCACACTGGGGAGAAACCTTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCGTAGTTC
AGGACTACGTTCACATCAAAGGACCCACACTAGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCTGA
AGGGAAGCTTACATACGCATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGTTTTGCT
CATAGTTTAGGACTACGTTCACATCAAAGAACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGCTT
TACTCAGAAGGGAAACTTACATACACATCAAAGAACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGA
GCTTTGCTCGTAGTTCAGGACTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGA
CAGAGCTTTGCTCGTAGTTCAGGACTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCATATAACTGCCTGGAGTG
TGGACAGAGCTTCACTCAGAAGGGACACTTACATACACATCAAAGAACTCACACTGGGGAGAAACCCTATAAATGCCTGG
AGTGTGGACAGAGCTTTGCTCGTAGTTCAGGACTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCATATAAATGC
CTGGAGTGTGGACAGAGCTTCACTCAGAAGGGAAACTTACATACGCATCAAAGGACTCACACTGGGGAGAAACCCTACAA
CTGCCTGGAATGTGGACAGAGTTTTGCTCATAGTTTAGGACTACGTTCACATCAAAGGACTCACACTGGGGAGGAACCCT
ATAACTGCCTGGAGTGTGGACAGAGCTTTACTCAGAAGGGAAACTTACATACACATCAAAGGACTCACACTGGGGAGAAA
CCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCGTAGTTCAGGACTACGTTCACATCAAAGGACTCACACTGGGGA
GAAACCCTATACATGCCTGGAGTGTGGACAGAGCTTCATTGATTGTTCAACTCTACGTAGACATCAAAGGACTCACACTG
GGGAGAAACCATATAACTGCCTGGAGTGTGGGCAGAGCTTCACTCAGAAGGGACACTTACATACACATCAAAGGACTCAC
ACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTTGCTCGTAGTTCAGGACTACGTTCACATCAAAGGAC
TCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCGAAGTTCAGGACTACGTTCCCATCAAA
GGACTCACACTGGGCAGAAACCATAG

Alignment

ORF - retro_acar_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 92.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKAYKCIECGKSFSHHGNLNRHQRTHTGEKSYKCLECGQSFTQSSGLRSHQRTHTGEKPYNCLECGQSFT
          EKAYKCIECGKSF.HHGNL.RHQRTHTGEKSYKCLECGQSFTQSSGLRSHQRTHTGEKPYNCLECGQSFT
Retrocopy EKAYKCIECGKSFIHHGNLKRHQRTHTGEKSYKCLECGQSFTQSSGLRSHQRTHTGEKPYNCLECGQSFT

Parental  QKGHLHTHQRTHTREKPYNCLECGQSFTQKGSLHTHRRTHTGEKPYNCLECGQSFAHSSALYSHQRTHTG
          QKGHLHTHQRTHT.EKPYNCLECGQSFTQKGSLHTH.RTHTGEKPYNCLECGQSFAHSSALYSHQRTHTG
Retrocopy QKGHLHTHQRTHTGEKPYNCLECGQSFTQKGSLHTHQRTHTGEKPYNCLECGQSFAHSSALYSHQRTHTG

Parental  EKPYKCLDCGQSFTQKGHLHTHQRTHTGEKPYNCLECGQSFAHSSALYSHQRTHTGEKPYKCLECGQSFT
          EKPYKCL.CGQSFTQKG.LHTHQRTHTGEKPYNCLECGQSFA.SS.L.SHQRTHT.EKPYKCLECGQSFT
Retrocopy EKPYKCLECGQSFTQKGSLHTHQRTHTGEKPYNCLECGQSFARSSGLRSHQRTHTREKPYKCLECGQSFT

Parental  QKGHLHTHQRTHTGEKPYNCLECGQSFTQKGSLHRHQRTHTGEKPFKCLECGQSFGRSSGLRSHQRTHTG
          .KG.LHTHQRTHTGEKPYNCLECGQSF.....L..HQRTHTGEKP..CLECGQSF.....L..HQRTHTG
Retrocopy LKGSLHTHQRTHTGEKPYNCLECGQSFAHSLGLRSHQRTHTGEKPYTCLECGQSFTQKGNLHTHQRTHTG

Parental  EKPYKCLECGQSFTQKKGNLHTHQRTHTGEKPYKCLECGQSFTQKGHLHTHQRTHTGEKPYKCLECGQSF
          EKPY.CLECGQSF....G.L..HQRTHTGEKPY.CLECGQSF.....L..HQRTHTGEKPY.CLECGQSF
Retrocopy EKPYNCLECGQSFARSSG-LRSHQRTHTGEKPYNCLECGQSFARSSGLRSHQRTHTGEKPYNCLECGQSF

Parental  TQKGHLHTHQRTHTGEKPYKCLECGQSFARSSGLRSHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHT
          TQKGHLHTHQRTHTGEKPYKCLECGQSFARSSGLRSHQRTHTGEKPY.CLECGQSFTQKG.LHTHQRTHT
Retrocopy TQKGHLHTHQRTHTGEKPYKCLECGQSFARSSGLRSHQRTHTGEKPYKCLECGQSFTQKGNLHTHQRTHT

Parental  GEKPYKCLECGQSFAQSSGLRSHQRTHTGEKPYKCLECGQSFARSSYLRKHHRIHIGEKPYKCLECGQSF
          GEKPY.CLECGQSFA.S.GLRSHQRTHTGE.PY.CLECGQSF.....L..H.R.H.GEKPY.CLECGQSF
Retrocopy GEKPYNCLECGQSFAHSLGLRSHQRTHTGEEPYNCLECGQSFTQKGNLHTHQRTHTGEKPYNCLECGQSF

Parental  TRKGSLQTHQRTHTGEKPYKCLECGQSFTCSSGLHSHQRTHTGEKPHKCLECEQSFTHSSGLRRHQRTHT
          .R...L..HQRTHTGEKPY.CLECGQSF...S.L..HQRTHTGEKP..CLEC.QSFT....L..HQRTHT
Retrocopy ARSSGLRSHQRTHTGEKPYTCLECGQSFIDCSTLRRHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHT

Parental  GEKPFKCLECEQSFTQSSGLRSHQRIHTGEKPYNCLECGQSFTRSSGLRSHQRTHTGEK
          GEKP.KCLEC.QSF..SSGLRSHQR.HTGEKPYNCLECGQSF.RSSGLRSHQRTHTG.K
Retrocopy GEKPYKCLECGQSFARSSGLRSHQRTHTGEKPYNCLECGQSFARSSGLRSHQRTHTGQK

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	0.46 RPM	2.23 RPM
SRP009831_brain	2.13 RPM	5.02 RPM
SRP009831_dewlap	1.48 RPM	1.94 RPM
SRP009831_embryo	2.22 RPM	7.56 RPM
SRP009831_heart	1.87 RPM	5.71 RPM
SRP009831_liver	0.04 RPM	0.94 RPM
SRP009831_lung	0.35 RPM	4.33 RPM
SRP009831_ovary	0.58 RPM	1.35 RPM
SRP009831_skeletal_muscle	0.11 RPM	0.62 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_13 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_13 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,