RetrogeneDB ID: retro_acar_94

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:128387117..128387825(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000012405
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TM7SF2
• Ensembl ID: ENSACAG00000010869
• Aliases: None
• Description: None

Sequence

>retro_acar_94
ATTGGCTCCTTCGACCTCAAGTTCTTTTGCGAGCTGAGACCCGGTCTCCTGGGATGGGCGGTGATCAACATGGGAATGCT
GATGAAGGAGGCGGAGGTCCGCGGCAGCCCCTCGCTGGCCATGGTCCTGGTCAACGGCTTCCAGCTGCTCTACGTGGTGG
ACGCTTTGTGGCACGAGGAGGCGGTCTTGACCACCATGGACATCCAGCGGGACGGCTTTGGCTTCATGCTGGCCTTTGGG
GACCTGGCCTGGGTGCCCTTCCTCTACAGCCTCCAGGGTCACTTCTTGGTCACTCACCCCCACAGGGTCAGCCTCCCTGC
GGCCGCCGGCATCATCCTCCTGAACGGCCTGGGCTACTCCATCTTCCGGGGCGCCAACTCCCAGAAGAACACTTTCCGAC
GCAACCCCAACGACCCCCGAGTGGCCGGGCTTCGCACGCTGCCCACGGCCACGGGGCGACGGCTGCTGGTGAGCGGGTGG
TGGGGCCTGGTGCGGCACCCCAACTACCTGGGGGACCTCCTCATGGCCTTGGCCTGGTCACTCACCTGCGGTCTGACCCA
CGCGCTGCCCTACTTCTACCCGGCCTACTTCCTGCTGCTGCTGCTGCACCGGGAGGCACGGGACGAGCGCCACTGCCTGC
GCCAGTACGGCCTGGCCTGGGGGGAGTATTGCCGGAAGGTCCCCTTCCGCATCCTGCCCTACGTTTAC

Alignment

ORF - retro_acar_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.15 %
• Parental protein coverage: 59.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGSFDLKFFCELRPGLLGWAVINMGMLMKEAEVRGSPSLAMVLVNGFQLLYVVDALWHEEAVLTTMDIQR
          IGSFDLKFFCELRPGLLGWAVINMGMLMKEAEVRGSPSLAMVLVNGFQLLYVVDALWHEEAVLTTMDIQR
Retrocopy IGSFDLKFFCELRPGLLGWAVINMGMLMKEAEVRGSPSLAMVLVNGFQLLYVVDALWHEEAVLTTMDIQR

Parental  DGFGFMLAFGDLAWVPFLYSLQGHFLVTHPHRVSLPAAAGIILLNGLGYSIFRGANSQKNTFRRNPNDPR
          DGFGFMLAFGDLAWVPFLYSLQGHFLVTHPHRVSLPAAAGIILLNGLGYSIFRGANSQKNTFRRNPNDPR
Retrocopy DGFGFMLAFGDLAWVPFLYSLQGHFLVTHPHRVSLPAAAGIILLNGLGYSIFRGANSQKNTFRRNPNDPR

Parental  VAGLRTLPTATGRRLLVSGWWGLVRHPNYLGDLLMALAWSLPCGLTHALPYFYPAYFLLLLLHREARDER
          VAGLRTLPTATGRRLLVSGWWGLVRHPNYLGDLLMALAWSL.CGLTHALPYFYPAYFLLLLLHREARDER
Retrocopy VAGLRTLPTATGRRLLVSGWWGLVRHPNYLGDLLMALAWSLTCGLTHALPYFYPAYFLLLLLHREARDER

Parental  HCLGQYGLAWGEYCRKVPFRILPYVY
          HCL.QYGLAWGEYCRKVPFRILPYVY
Retrocopy HCLRQYGLAWGEYCRKVPFRILPYVY

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	0.07 RPM	1.44 RPM
SRP009831_brain	1.70 RPM	18.60 RPM
SRP009831_dewlap	0.04 RPM	3.37 RPM
SRP009831_embryo	0.62 RPM	5.01 RPM
SRP009831_heart	0.05 RPM	1.40 RPM
SRP009831_liver	0.12 RPM	0.65 RPM
SRP009831_lung	1.16 RPM	6.60 RPM
SRP009831_ovary	0.15 RPM	2.28 RPM
SRP009831_skeletal_muscle	0.04 RPM	0.87 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_94 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_94 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010869	1 retrocopy	retro_acar_94 ,