RetrogeneDB ID: retro_acar_127

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:131651753..131652432(+)
• Located in intron of: ENSACAG00000003745

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM3B
• Ensembl ID: ENSACAG00000001496
• Aliases: None
• Description: None

Sequence

>retro_acar_127
TTGGGAGGATTTATCATTGCATCTTTCTGTGCCTGGTACTTGGGGTCTCTTTTAGCATATATAATACCTAAAGACTCAAT
AATGACAACTTAACGACAATCTTCAGAACCTTGCCAAAAAACCAAAAATTGTGGTTCCATCCCTTAAAAGACACAAATGT
GACCAGTGGTCTCCATGTCCGTCTTGAAGCTATGCTTATCGCATACTCAGTGGTGGGGGCAAGGAGAAATTTGCTAAAAT
TTGTTTTGAAGATGAACTGATCATAAGTGAAGAAAAAGGGAATGTTGGAAGAGGAATAAATATTGCAGTTGTAGACTATG
ACGCTGGAAAGGTTGTTGCTGCAAAATATTTTGACATGTGGAAAGGGGAATTCTCTGGACCAATGACTGATTTCATCAGA
AAGGCCCCCTTGAGGTCACTGCTCCTGATGGTAACCCATAATGATGGAAGTAGCAGGTTAAAGGAGGATGGGAAAAAGGC
AATTGCTGAACTAGGAAGTAAAGAAATACGAAATTTGAAATTTAGATCAAGCTAGGTCTTCATAGCAGGAAAAGGTTTTA
AGCTACCAGAAAATATAGAAAAGGAAAAGTTCAACTATTCTGACATGAATAAGAACCGATACAGTGGCTGGCCAGCTGAA
ATCCAGATAGAAGGCTGTATTCCAAAGAACATGACAAAC

Alignment

ORF - retro_acar_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.83 %
• Parental protein coverage: 95.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGGFIIASFCAWYLGSLLAYIIPEDSIMTT-YDNLQNLAKKPKIVVPSPKRHKCDQWSPCPSQSYAYRIL
          LGGFIIASFCAWYLGSLLAYIIP.DSIMTT..DNLQNLAKKPKIVVPS.KRHKCDQWSPCPS.SYAYRIL
Retrocopy LGGFIIASFCAWYLGSLLAYIIPKDSIMTT>NDNLQNLAKKPKIVVPSLKRHKCDQWSPCPS*SYAYRIL

Parental  SGGGKEKFAKICFEDELIISEEKGNVGRGINIAVVNYDTGKVFAAKYFDMWEGEFSGPMTDFIRKAPLRS
          SGGGKEKFAKICFEDELIISEEKGNVGRGINIAVV.YD.GKV.AAKYFDMW.GEFSGPMTDFIRKAPLRS
Retrocopy SGGGKEKFAKICFEDELIISEEKGNVGRGINIAVVDYDAGKVVAAKYFDMWKGEFSGPMTDFIRKAPLRS

Parental  LLLMVTHDDGSSRLKEDGKKAIAELGSKEIRNLKFRSSWVFIAGKGFKLPENIENEKINHSDMNKNRYSG
          LLLMVTH.DGSSRLKEDGKKAIAELGSKEIRNLKFRSS.VFIAGKGFKLPENIE.EK.N.SDMNKNRYSG
Retrocopy LLLMVTHNDGSSRLKEDGKKAIAELGSKEIRNLKFRSS*VFIAGKGFKLPENIEKEKFNYSDMNKNRYSG

Parental  WPAEIQIEGCIPKNMTN
          WPAEIQIEGCIPKNMTN
Retrocopy WPAEIQIEGCIPKNMTN

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	17.59 RPM
SRP009831_brain	0.05 RPM	1.09 RPM
SRP009831_dewlap	0.04 RPM	23.20 RPM
SRP009831_embryo	0.03 RPM	1.81 RPM
SRP009831_heart	0.47 RPM	10.79 RPM
SRP009831_liver	0.00 RPM	36.36 RPM
SRP009831_lung	0.10 RPM	39.84 RPM
SRP009831_ovary	0.08 RPM	19.46 RPM
SRP009831_skeletal_muscle	0.00 RPM	15.84 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_127 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_127 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001496	1 retrocopy	retro_acar_127 ,
Myotis lucifugus	ENSMLUG00000014543	1 retrocopy	retro_mluc_2488,