RetrogeneDB ID: retro_acar_17

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343290.1:1358385..1358952(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000015512
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000014643
• Aliases: None
• Description: None

Sequence

>retro_acar_17
GGGAATCCGGTCCTGAAATTCATCCACAACGTGCCTTGGGAGTTTGGAGACATCGTCCCTGATTATTTGCTGGGCCAAAG
CACCTGCGCCCTTTTCCTAAGCTGCCGCTACCACAACCTGAACCCCAATTACATCCACGATCGGCTCCGCAACCTGGGAA
AGACCTATGCACTGCAGGCGTTTCTGCTTCAGGTCGACGTGAAAGATCCACACCGGGCTCTCAAAGATCTGGCCAAGATC
TACATCCTTTCCAGCTGCACCTTGATCCTGGTCTGGAGCCCAGAGGAAGCGGGCCGCTACTTGGAGACGTACAAAGCCTA
CGAGCAAAAGCCGGCTGACCTCTTGAAGGAGAAAGTGGACAAGGACTACCTGTCGAGAATGACCGACTGCCTGACCAGCG
TGAAGTCAGTGAACAAGACGGGCACGCTGAGCCTTCTCTCCAACTTCAAATCTCTGGCCAACCTTGTGCAAGCCTCGAAG
GAGGACCTGTCTCTCTGCCCAGGGATCGGGCCACAAAAGGCCAAGAGGCTCTTCGATACTCTCCATGAACCTTTCTTCAA
GCTTCCC

Alignment

ORF - retro_acar_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.18 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNPVLKFIRNVPWEFGDIVPDYLLGQSTCALFLSLRYHNLNPNYIHDRLRNLGKTYALQVLLLQVDVKDP
          GNPVLKFI.NVPWEFGDIVPDYLLGQSTCALFLS.RYHNLNPNYIHDRLRNLGKTYALQ..LLQVDVKDP
Retrocopy GNPVLKFIHNVPWEFGDIVPDYLLGQSTCALFLSCRYHNLNPNYIHDRLRNLGKTYALQAFLLQVDVKDP

Parental  HRALKDLAKICILSSCTLVLAWSPEEAGRYLETYKAYEQKPADLLKEKVDKDYLSRMTDCLTSVKSVNKT
          HRALKDLAKI.ILSSCTL.L.WSPEEAGRYLETYKAYEQKPADLLKEKVDKDYLSRMTDCLTSVKSVNKT
Retrocopy HRALKDLAKIYILSSCTLILVWSPEEAGRYLETYKAYEQKPADLLKEKVDKDYLSRMTDCLTSVKSVNKT

Parental  DTLSLLSNFKSLANLVQASKEDLSLCPGIGPQKAKRLFDALHEPFYKHP
          .TLSLLSNFKSLANLVQASKEDLSLCPGIGPQKAKRLFD.LHEPF.K.P
Retrocopy GTLSLLSNFKSLANLVQASKEDLSLCPGIGPQKAKRLFDTLHEPFFKLP

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	23.04 RPM
SRP009831_brain	0.00 RPM	16.52 RPM
SRP009831_dewlap	0.00 RPM	22.27 RPM
SRP009831_embryo	0.03 RPM	23.98 RPM
SRP009831_heart	0.00 RPM	63.04 RPM
SRP009831_liver	0.04 RPM	38.04 RPM
SRP009831_lung	0.05 RPM	39.64 RPM
SRP009831_ovary	0.04 RPM	19.81 RPM
SRP009831_skeletal_muscle	0.00 RPM	81.80 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_17 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_17 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014643	2 retrocopies	retro_acar_17 , retro_acar_175,
Canis familiaris	ENSCAFG00000004448	1 retrocopy	retro_cfam_776,