RetrogeneDB ID: retro_acar_141

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 5:104228118..104228466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTSF1L
• Ensembl ID: ENSACAG00000029590
• Aliases: None
• Description: gametocyte specific factor 1-like [Source:HGNC Symbol;Acc:16198]

Sequence

>retro_acar_141
ATGGATCCGGAAAAACTCTTGCAGTGCCCCTATGACAAGAACCACCAGATCAGAGCCTCCAGGTTTCCTTATCATTTGGT
GAAATGCAAGAAAAACAACGAGAAGATTGCCAAACAACTAGTAACGTGCCCCTACAATGCCCGTCACAGAATTCCTAAGG
ACGAGTTCAACTCACACATTGAAATCTGTGAAAGTAAAATTTCCTCCGAGGTGAATAAAGTTGCAGCAAAGAATGGAAGC
AAAGAAAAGACAGCCTGGAAATGCCCCTCTCCATAGGAAGACTGGGAAGCTGATGCCGATGAAGCTTCTGTTAGTCCTTT
TGTTTTTGGTGCCAGAATGTCAGAGAAT

Alignment

ORF - retro_acar_141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDPETLLQCPYDKNHQIRASRFPYHLVKCKKNNQKIAKQLATCPYNARHRIPKDEFNFHIEICESKISLE
          MDPE.LLQCPYDKNHQIRASRFPYHLVKCKKNN.KIAKQL.TCPYNARHRIPKDEFN.HIEICESKIS.E
Retrocopy MDPEKLLQCPYDKNHQIRASRFPYHLVKCKKNNEKIAKQLVTCPYNARHRIPKDEFNSHIEICESKISSE

Parental  VNKAAVKNGSKEKTASKCPSPQEDWEDDADKTPTRPFVFGASISEN
          VNK.A.KNGSKEKTA.KCPSP.EDWE.DAD.....PFVFGA..SEN
Retrocopy VNKVAAKNGSKEKTAWKCPSP*EDWEADADEASVSPFVFGARMSEN

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	3.58 RPM
SRP009831_brain	0.00 RPM	0.38 RPM
SRP009831_dewlap	0.00 RPM	43.03 RPM
SRP009831_embryo	0.00 RPM	1.01 RPM
SRP009831_heart	0.00 RPM	0.26 RPM
SRP009831_liver	0.00 RPM	1.10 RPM
SRP009831_lung	0.00 RPM	0.65 RPM
SRP009831_ovary	0.00 RPM	36.64 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_141 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_141 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014260	3 retrocopies	retro_acar_135, retro_acar_143, retro_acar_92,
Anolis carolinensis	ENSACAG00000029590	1 retrocopy	retro_acar_141 ,
Ailuropoda melanoleuca	ENSAMEG00000000958	1 retrocopy	retro_amel_91,
Cavia porcellus	ENSCPOG00000023851	1 retrocopy	retro_cpor_93,
Felis catus	ENSFCAG00000031316	1 retrocopy	retro_fcat_1,
Mustela putorius furo	ENSMPUG00000005664	1 retrocopy	retro_mputfur_116,
Mus musculus	ENSMUSG00000053508	1 retrocopy	retro_mmus_199,
Rattus norvegicus	ENSRNOG00000036830	1 retrocopy	retro_rnor_1938,