RetrogeneDB ID: retro_acar_118

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:40653001..40653438(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000025593
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000013688
• Aliases: None
• Description: None

Sequence

>retro_acar_118
ATGCTAAAGAGAAAGCAGCAGTTGGTGGACATCATTGAGAAGGTGAAACCCAAGATCCAACTGCTGATTGAGAAATGCAA
CCTGGTCAAAATGTGGGTGCAGTATTGATCCCCAGGATAGAAGGTGGCAATAATTTGGATGTTTCTATTCAGGAAGAAAC
TGTGGCTGAACTCTGGCCTGTGGAGAGTGAGGCAGCTTCATACTTGGACCAGATCTCTAGATATTACATCACATGGACAA
AGCTAGTTTCTAAAATAGCAAAATATCCTCATGTGGAGGATTGCCATTGCACAGTGACTGAAATGGATGAAAAGGAATAT
ATCAGTCTGCGACTCATCATTTCAGAGCTGAGAAATCAATATGTGACCCAGCACATCATGACCCTGAAGAACATTGAGAA
GATCAAGTGACCCTGGAGCAGAAATGCAGAGACTCTA

Alignment

ORF - retro_acar_118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQ-LLIPRIEDGNNFGVSIQEETVAELRTVESEAASYL
          MLK..QQLVDIIEKVKP.I.LLIEKCN.VKMWVQ..LIPRIE.GNN..VSIQEETVAEL..VESEAASYL
Retrocopy MLKRKQQLVDIIEKVKPKIQLLIEKCNLVKMWVQ<VLIPRIEGGNNLDVSIQEETVAELWPVESEAASYL

Parental  DQISRYYITRAKLVSKIAKYPHVEDYRRTVTEMDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPR
          DQISRYYIT..KLVSKIAKYPHVED...TVTEMDEKEYISLRLIISELRNQYVT.H.M.LKNIEKIK.P.
Retrocopy DQISRYYITWTKLVSKIAKYPHVEDCHCTVTEMDEKEYISLRLIISELRNQYVTQHIMTLKNIEKIK*PW

Parental  SSNAETL
          S.NAETL
Retrocopy SRNAETL

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	19.89 RPM
SRP009831_brain	0.00 RPM	18.32 RPM
SRP009831_dewlap	0.00 RPM	39.95 RPM
SRP009831_embryo	0.00 RPM	69.86 RPM
SRP009831_heart	0.00 RPM	24.80 RPM
SRP009831_liver	0.00 RPM	19.76 RPM
SRP009831_lung	0.05 RPM	16.93 RPM
SRP009831_ovary	0.00 RPM	46.06 RPM
SRP009831_skeletal_muscle	0.00 RPM	34.75 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_118 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_118 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118 , retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249, retro_btau_941,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,