RetrogeneDB ID: retro_acar_149

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 6:68412454..68413048(-)
• Located in intron of: ENSACAG00000003485

Retrocopy information

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

Parental gene information

• Parental gene symbol: aca-mir-5408a
• Ensembl ID: ENSACAG00000001053
• Aliases: None
• Description: aca-mir-5408a [Source:miRBase;Acc:MI0018911]

Sequence

>retro_acar_149
ATGTCGGCCTTTGGTTTCGCTCGGTTCGGGGCGGGAGGCGCTTACTCGAGTTCTCAATTAATCTGGAACATTCAGCATCC
AGCAAACCACTGGCAGTCATCACTTCTCGGACTGAGGGCTGCTCTCCCCATGAGAGCAGAACCAAAGAAAAAGAAGAAGG
TGGATCCAAAGAGAGAACTTGCCATTAGGGACCGGATGAAGAAAAAGATTAAAAAATTGGAAAAGGCTCCTCAGGAATTG
ATTCCCATTGAAGACTTTGTAACACCATTCCGATTCATGGATGAAAGAAAAGTGCGAGCCATCTCTCCCCTGCCTTTTGA
GGAGAGCGAAAAGCGAGCATTGCTTTTGAAGAAGTGGGTGGTATACAAGCAAGTGCAGCACAAGGCAGAGATGGAGGCAG
CCAGGTCCCTGGTGGAGGCCCAAGAAGAGGCCTTAAAAGAACTGTGCCTCGAATCGGAGGAGCTGTATCAGGCAGCTGTT
TGGCGGGATGAATGGCTGTTCCCTTTTGAGAGGCAGGAGCCAACCCACACACCGCCAGTGCCAAAGTATGAGGCTCTTGA
AGGGAGGTGTAATGACATCACTAAAGTTTATACC

Alignment

ORF - retro_acar_149 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.86 %
• Parental protein coverage: 99. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSALCFARIGAGSASLSSQLIWNIQHRANHWQSSLLGLRAALPMRAEPKKKKKVDPKREIAIRDRMKKKI
          MSA..FAR.GAG.A..SSQLIWNIQH.ANHWQSSLLGLRAALPMRAEPKKKKKVDPKRE.AIRDRMKKKI
Retrocopy MSAFGFARFGAGGAYSSSQLIWNIQHPANHWQSSLLGLRAALPMRAEPKKKKKVDPKRELAIRDRMKKKI

Parental  KKLEKAPQELIPIEDFITPFRFMDETRVRDISPLSFEESERRALLLKKWTVYKQAQNKAEMKAAKALMEA
          KKLEKAPQELIPIEDF.TPFRFMDE..VR.ISPL.FEESE.RALLLKKW.VYKQ.Q.KAEM.AA..L.EA
Retrocopy KKLEKAPQELIPIEDFVTPFRFMDERKVRAISPLPFEESEKRALLLKKWVVYKQVQHKAEMEAARSLVEA

Parental  QEEALKELRLESEELYQAAIQRDEGLFPFERQEPTHTPPVSKYEAPEGRCHDITKVYT
          QEEALKEL.LESEELYQAA..RDE.LFPFERQEPTHTPPV.KYEA.EGRC.DITKVYT
Retrocopy QEEALKELCLESEELYQAAVWRDEWLFPFERQEPTHTPPVPKYEALEGRCNDITKVYT

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	1.81 RPM	27.18 RPM
SRP009831_brain	1.85 RPM	32.14 RPM
SRP009831_dewlap	6.20 RPM	59.65 RPM
SRP009831_embryo	4.45 RPM	42.20 RPM
SRP009831_heart	3.32 RPM	33.00 RPM
SRP009831_liver	1.39 RPM	29.29 RPM
SRP009831_lung	2.42 RPM	16.42 RPM
SRP009831_ovary	6.33 RPM	50.65 RPM
SRP009831_skeletal_muscle	12.16 RPM	26.88 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_149 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_149 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149 ,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,