RetrogeneDB ID: retro_acar_158

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343209.1:1224665..1225055(-)
• Located in intron of: ENSACAG00000008892

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000022172
• Aliases: None
• Description: None

Sequence

>retro_acar_158
TTCTTCCAAGGGGAGAGCTTTGACTACATTGGCAGTTCTCGCATGGTGTATGATATGCAGAATGAAAAGTTCCTTATTGG
CCTGGATAACATCCATTCCTTCATGGAGCTGAGTCGGGTTGCACTCAGGAATGGCTCAGATTTGTGGATGCATATAGATC
CTGTCTCTCAGAAGAACCACTCTGTTAACACGACCGTCAAAAACATGGTGAAGATGCTGAAAAGCAGCAGCCAAAACACC
AACGTGGTAATGAATGAGATCGGATTGACCCAGCCACTTCCACCATCTTCCTTCTAGCATTTCCTAAGGGCCAGGCAGCT
CCCAGGACTGGTATTAGCTAACCACCACTCCACTTTTCACAACAGGTACTACCAGAGCATCTATGACACA

Alignment

ORF - retro_acar_158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.46 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLFQETFDYIGSSRMVYDMQNGKFPIKLDNIHSFLEISQVALRNGSDLWMHTDPVSQRNQSLQGSIQTML
          F...E.FDYIGSSRMVYDMQN.KF.I.LDNIHSF.E.S.VALRNGSDLWMH.DPVSQ.N.S.......M.
Retrocopy FFQGESFDYIGSSRMVYDMQNEKFLIGLDNIHSFMELSRVALRNGSDLWMHIDPVSQKNHSVNTTVKNMV

Parental  GALKNMSVGTPLSLREIGLTQPLPPSSFQRFLRARPIPGVVLADHQTTFHNRYFQSIYDT
          ..LK..S..T.....EIGLTQPLPPSSF..FLRAR..PG.VLA.H..TFHNRY.QSIYDT
Retrocopy KMLKSSSQNTNVVMNEIGLTQPLPPSSF*HFLRARQLPGLVLANHHSTFHNRYYQSIYDT

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	0.03 RPM	0.82 RPM
SRP009831_brain	0.00 RPM	4.97 RPM
SRP009831_dewlap	0.00 RPM	9.03 RPM
SRP009831_embryo	0.12 RPM	2.49 RPM
SRP009831_heart	0.05 RPM	6.69 RPM
SRP009831_liver	0.00 RPM	3.07 RPM
SRP009831_lung	0.25 RPM	4.18 RPM
SRP009831_ovary	0.08 RPM	12.51 RPM
SRP009831_skeletal_muscle	0.04 RPM	1.57 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_158 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_158 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016223	1 retrocopy	retro_acar_159,
Anolis carolinensis	ENSACAG00000022172	1 retrocopy	retro_acar_158 ,