RetrogeneDB ID: retro_acar_136

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 5:127596595..127597086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSACAG00000005134
• Aliases: None
• Description: None

Sequence

>retro_acar_136
ATGGCTCTGTCAGGCTTGATCCAGACCTTTAGGTCATGCTGCTGTCTTCCAGCCACCATCTCACAAGGATACCTGTGTCC
TCTATGCCCATTTCTCTAGCAAGTGAACTCCAAATCCGCCATGAAATTGGGACTTCTGCCATGGTGTCTGCTAGAGATAT
GCTGTGGAAATGCAGGACCAAGTACATCATAAAGCCCATTCCTTTAAGAAAAACAGGAGGCTGAGATCACACAGGACGTA
TCAGTGTGCATGGAATTGGGGGAGGAAGGAAGCAGTGCTACCGTATGATTGATTTCCGAAGATTGAATTATGAAGAAGGA
ACAGAGCCTGGTCCATTTGATGAGAAAGTGATTCAGGTCTGGTATGATCAATGCCAGTCAGCCGATATAGATCTGGTAGC
TGCAGGGAAGCGGAAACGCTGGATCATTGCAACAGAAAACATGGAAGTTGGTGACATCATCAAAACGTCAGGACACACAG
GCAGTCTCAGC

Alignment

ORF - retro_acar_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.09 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTLSGLIQTFRS-LLLSSSPHLTRIPVSSMPISLASQLQIRHEIGTSAVVSARDMLWKCRTKYTIKPIPL
          M.LSGLIQTFRS..LLSSS.HLTRIPVSSMPISLAS.LQIRHEIGTSA.VSARDMLWKCRTKY.IKPIPL
Retrocopy MALSGLIQTFRS<MLLSSSHHLTRIPVSSMPISLASELQIRHEIGTSAMVSARDMLWKCRTKYIIKPIPL

Parental  RKTGGRDHTGRISVHGIGGGRKQCYRMIDFRRLNYEEGTEPGPFDEKVVQVRYDPCRSADIALVAGGKRK
          RKTGG.DHTGRISVHGIGGGRKQCYRMIDFRRLNYEEGTEPGPFDEKV.QV.YD.C.SADI.LVA.GKRK
Retrocopy RKTGG*DHTGRISVHGIGGGRKQCYRMIDFRRLNYEEGTEPGPFDEKVIQVWYDQCQSADIDLVAAGKRK

Parental  RWIIATENMEVGDIIKTSGHIGRMA
          RWIIATENMEVGDIIKTSGH.G...
Retrocopy RWIIATENMEVGDIIKTSGHTGSLS

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	47.66 RPM
SRP009831_brain	0.00 RPM	35.51 RPM
SRP009831_dewlap	0.00 RPM	72.48 RPM
SRP009831_embryo	0.00 RPM	52.99 RPM
SRP009831_heart	0.00 RPM	52.09 RPM
SRP009831_liver	0.00 RPM	50.96 RPM
SRP009831_lung	0.00 RPM	42.31 RPM
SRP009831_ovary	0.00 RPM	61.93 RPM
SRP009831_skeletal_muscle	0.00 RPM	60.79 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_136 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_136 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136 ,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,