RetrogeneDB ID: retro_acar_18

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343777.1:32906..34868(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000028936
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000026260
• Aliases: None
• Description: None

Sequence

>retro_acar_18
ATGGAAAGCGATAAAAAGAATGAAGGCCTGAAAAGCCAACCCGATGAAGCACAGCAAACACATGGAAACAAGTGGCGTGT
TGTCGAAAATAATTTGCTCGAGCCTTCAATAGGAGGAGGCTCTCATGACGAATCTGAAAGGTGTACGGATGACGACGCGG
ATCTCCTCTTGGTTTGCTCTGAATGTGGGAAATGCTTCGTCCATCCGGCGGATCTTACGAAACACGAGAAAACTCATATC
GGAGGGGAAGAGGATCCAAAGCAATTGACTCGCAGCTCGGACCAAGTACTTCCTACGAGCGAATGTCCCTATAAATGTAA
AATTTGCGGAAATGCTTTCGAGAAGCGCGAGAGACTCGTCCAACATCAGAGGAAGCACGAGAAAAAGCCCTGCCAGTGCT
TGGAGTGCAAGAAAGCCTTTGGTGACGTCAAAACGCTTCAAGCGCATCAAAGGATGTATAGAAATATGAACGCTGAGCGC
AGAGAAAGCCGTAGCCAGCTTTTCAGCCTTTTCGCTTTTCAGAATATGTTTTTGGGTGAGAAAACTTACAAAGGCACAGA
GTCCGGGAAGCGGTTCAAAAGCAGGACGCTTCTTGAAGCACACCCGAGGATCCACACAAGCGAGAGGCCTTCTGAGCTTG
GAAGAAGCACTCCCATGAGCGAGAAAACCCGTGAAGGCCTGCAGAATGGGAAGAACGTCTCTCATCTCGCAAATCTTCAA
TCCAGTTTAAAGGCACATGCCGCGGAGAAGCGCTATGGCTGTCCCAAGTGCCCCAAGACCTTCGCTTCCAGGGAACAATC
TACATCCCACCAAAGGAATCACACATGCGAGAAACCTTATAAATGCCCCGACTGCGGGAAGAGCTTTGCCTGGATTTTTC
ACCTTAAGGCGCATCGGGCCATCCACGCGGCGGAGAAACCCTATAAATGCTCTGATTGTGGAGAAAGCTTCGTCCAGGAT
TCACATTTAAAGGCACACCAAAGAAAGCACACAGGAGAGAAGCCCTATAAATGCTCCGATTGTGGAGAAAGCTCCGTCCA
GGATTCACATTTAAAGGCACACCAAAGAAAGCACACAGGAGAGAAGCCCTATAAATGCTCCGACTGTGGGGAAAGCTTCG
TCCAGGATTCACATTTAAAGGCACACCAAAGAAAGCACACAGGAGAGAAGCCCTATAAATGCTCCGACTGTGGGGAAAGC
TTCGTCCAGGATTCACATTTCAAGGCACACCAAAGAACCCACCATGCAGGAGAGAAGCCCTACAAATGCTCCGACTGTGG
GGAAAGCTTCGTCCAGGATTCGCATTTAAAGGCACACCAAAGAACGCATACAGGAGAGAAACCCTATAAATGCTCCGACT
GTGGGGAAAGCTTCGTCCAGGATTCGCATTTAAAGGCACACCAAAGAACGCATAGAGGAGAGAAACCCTATAAATGCTCC
GACTGTGGGGAAAGCTTCGTCCAGGATTCACATTTAAAGGCACACCAAAGAACGCACCACGCAGGAGAGAAACCCTACAA
ATGCTCCGACTGTGGGGAAAGCTTCGTCCAGGATTCGCATTTAAAGGCACACCAAAGAACACACCATGCAGGAGAGAAAC
CCTACAAATGCTCCGATTGTGGAGAAAGCTTCGTCCAGGATTCACATTTAAAGGCACACCAAAGAAAGCACACAGGAGAG
AAGCCCTATAAATGCTCCGACTGTGGGGAAAGCTTCGTCCAGGATTCACATTTAAAGGCACACCAAAGAACGCACCACGC
AGGAGAGAAGCCCTACAAATGCTTAGGCTGCGGGAAGAGTTTCAGCCGCAGCTCAGAATGGAAGGAGCACCAACGAATCC
ACGCAAAGGAGAAGCCTTTTAAATGCCTGATAAATAACTGCGGAAAGGGGTTCTGCGGTGTGAAAAATCTCAAAAAGCAT
CAGAGGAATTTCCATCGGCAATCGACCGGTCCCAAGGAGTGA

Alignment

ORF - retro_acar_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.18 %
• Parental protein coverage: 86.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLNTHQRTHTGEKPYNCLECGQSFACSSGLRSHQRTHTGEKPYNCLECGQSFTQSSGLRVHQSTHTGEKP
          NL......H..EK.Y.C..C...FA......SHQR.HT.EKPY.C..CG.SF.....L..H...H..EKP
Retrocopy NLQSSLKAHAAEKRYGCPKCPKTFASREQSTSHQRNHTCEKPYKCPDCGKSFAWIFHLKAHRAIHAAEKP

Parental  YKCLECGQSFTRKGNLLTHQRTHTGEKPYKCLECGQSFVHSSSLRSHQMTHTGEKPCKCLECGQSFARSG
          YKC..CG.SF.....L..HQR.HTGEKPYKC..CG.S.V..S.L..HQ..HTGEKP.KC..CG.SF....
Retrocopy YKCSDCGESFVQDSHLKAHQRKHTGEKPYKCSDCGESSVQDSHLKAHQRKHTGEKPYKCSDCGESFVQDS

Parental  ALRLHQSTHTGEKPYKCRECGQSFAHSSDLRSHQRTHHTGEKPYNCLECGQSFTQNSALRRHQRIHTGEK
          .L..HQ..HTGEKPYKC..CG.SF...S....HQRTHH.GEKPY.C..CG.SF.Q.S.L..HQR.HTGEK
Retrocopy HLKAHQRKHTGEKPYKCSDCGESFVQDSHFKAHQRTHHAGEKPYKCSDCGESFVQDSHLKAHQRTHTGEK

Parental  PYNCLECGQRFTQKGHLHSHQRTHTGEKPYNCLECGQSFTHSSGLRSHQWT-HTGEKPYKCLECGQSFAQ
          PY.C..CG..F.Q..HL..HQRTH.GEKPY.C..CG.SF...S.L..HQ.T.H.GEKPYKC..CG.SF.Q
Retrocopy PYKCSDCGESFVQDSHLKAHQRTHRGEKPYKCSDCGESFVQDSHLKAHQRTHHAGEKPYKCSDCGESFVQ

Parental  SGNLRSHQRT-HTGEKPYKCLECGQSFSHNSHLHRHQRTHTGEKPYKCLECGQSFAQSGNLRSHQRT-HT
          ...L..HQRT.H.GEKPYKC..CG.SF...SHL..HQR.HTGEKPYKC..CG.SF.Q...L..HQRT.H.
Retrocopy DSHLKAHQRTHHAGEKPYKCSDCGESFVQDSHLKAHQRKHTGEKPYKCSDCGESFVQDSHLKAHQRTHHA

Parental  GEKPYKCLECGQSFSHNSHLHRHQRTHTGEKPYKCL--ECGQSFARSGNLRSHQ
          GEKPYKCL.CG.SFS..S....HQR.H..EKP.KCL...CG..F....NL..HQ
Retrocopy GEKPYKCLGCGKSFSRSSEWKEHQRIHAKEKPFKCLINNCGKGFCGVKNLKKHQ

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	0.00 RPM	0.07 RPM
SRP009831_brain	0.09 RPM	0.80 RPM
SRP009831_dewlap	44.84 RPM	2.95 RPM
SRP009831_embryo	0.36 RPM	0.30 RPM
SRP009831_heart	0.00 RPM	0.31 RPM
SRP009831_liver	0.00 RPM	0.00 RPM
SRP009831_lung	0.20 RPM	0.05 RPM
SRP009831_ovary	56.02 RPM	2.20 RPM
SRP009831_skeletal_muscle	0.04 RPM	0.04 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_18 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_18 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000026260	1 retrocopy	retro_acar_18 ,
Cavia porcellus	ENSCPOG00000004610	1 retrocopy	retro_cpor_99,
Monodelphis domestica	ENSMODG00000023632	1 retrocopy	retro_mdom_7,