RetrogeneDB ID: retro_acar_190

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343420.1:253669..254061(+)
• Located in intron of: ENSACAG00000008413

Retrocopy information

• Ensembl ID: ENSACAG00000008453
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FABP9
• Ensembl ID: ENSACAG00000013564
• Aliases: None
• Description: None

Sequence

>retro_acar_190
ACAATGGAACAGTTTTTGGGAACTTGGAAGTTGGTTGCCAGTGAAAAATTTGATGACTACATGAAAGAAATTGGTGTGGG
CTTTGCCACCAGGAAGATAGCTGGTGTCGCCAAACCCAATGTCATCATCAGTTGCAATGAGGATGTCATAACATCAGAAC
AGATAGTAGTTTCAAGAACACAGAGCTTTCTTTCAAACTGGGGGATGAATTTGATGAAACCACAGCAGGTGACAGGAAAG
TAAAGAGTCTTGTGACATTAGACAATGATGTGTTGGTCCACTTGCAGAAATGGCATGGCAAGGAGACCACACTGAAAAGG
AAAATAGAAGATGGAAAGTTGGTTTTGGAATGCACTGCGAATGGCGTTGTCTCCACTAGAGTCTATGAGAAA

Alignment

ORF - retro_acar_190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 85.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TMEQFLGTWKLVASEKFDDYMKEIGVGFATRKIAGVAKPNVIISCNGDVIT-IRTESSFKNTELSFKLGE
          TMEQFLGTWKLVASEKFDDYMKEIGVGFATRKIAGVAKPNVIISCN.DVIT.IRT.SSFKNTELSFKLG.
Retrocopy TMEQFLGTWKLVASEKFDDYMKEIGVGFATRKIAGVAKPNVIISCNEDVIT<IRTDSSFKNTELSFKLGD

Parental  EFDETTADDRKVKSLVTLDNGVLVHLQKWDVKETTLKRKIEDGKLVLECTANGIVSTRVYEK
          EFDETTA.DRKVKSLVTLDN.VLVHLQKW..KETTLKRKIEDGKLVLECTANG.VSTRVYEK
Retrocopy EFDETTAGDRKVKSLVTLDNDVLVHLQKWHGKETTLKRKIEDGKLVLECTANGVVSTRVYEK

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	0.30 RPM	48.58 RPM
SRP009831_brain	0.00 RPM	1.33 RPM
SRP009831_dewlap	0.67 RPM	1113.48 RPM
SRP009831_embryo	0.15 RPM	10.28 RPM
SRP009831_heart	0.83 RPM	336.30 RPM
SRP009831_liver	0.25 RPM	122.42 RPM
SRP009831_lung	0.30 RPM	85.84 RPM
SRP009831_ovary	3.20 RPM	1188.17 RPM
SRP009831_skeletal_muscle	0.11 RPM	26.55 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_190 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_190 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013564	1 retrocopy	retro_acar_190 ,
Canis familiaris	ENSCAFG00000025410	3 retrocopies	retro_cfam_132, retro_cfam_137, retro_cfam_228,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Macaca mulatta	ENSMMUG00000010906	1 retrocopy	retro_mmul_1311,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,