RetrogeneDB ID: retro_acar_180

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343341.1:277381..277900(+)
• Located in intron of: ENSACAG00000004273

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPV17L2
• Ensembl ID: ENSACAG00000027644
• Aliases: None
• Description: None

Sequence

>retro_acar_180
TTCTACACACCACTTTTTGGAGGCCGCAACCTTATCATTACCAATACAGTGAGCTGTGGTGTTTTACTGGGAACTGCAGA
TATAATTCAGCAATCTTTGGAGAGAAGAAGAAACCCTGCACTGAAGTGGGATGCTGACCGCATGATACACATGTTCATTA
CAGGATGTTCCATGGGACCACCCCTACATTACTGGTACCTCTTGCTAGACAAAATAACCCCAGGAAAAGGAATGCAACAC
GTAAAAATTGTTGTCCTAAAGGTAACAATTGATCAGGCCTTTGCTCCATTCTTTGGATGCTGGTATTTCACATGGATGGG
ATTGCTTCAAGGTCATAGTTTGGCAGACAGTCTGAAGGAATTTAAAGAGAAGTTCTGGGAGTATTTCATTGCAGAACTCA
CTGTGTGGCCAGCTGCTCAACTGGTAAATTTTTTCTTTCTCCAGCCAAAATATCGAGTGATATTTGTGAACATGGTGACT
TTAGGATGGAATGTATACCTTTCATATCTCAAACACAGA

Alignment

ORF - retro_acar_180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.57 %
• Parental protein coverage: 87. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FWRPLFRGRLLLLTNTLSCGGLLAAGDTLRQAWERRKRSGRQVSLLSAARMFAIGCSMGPLMHYWYLWLD
          F..PLF.GR.L..TNT.SCG.LL...D...Q..ERR..............MF..GCSMGP..HYWYL.LD
Retrocopy FYTPLFGGRNLIITNTVSCGVLLGTADIIQQSLERRRNPALKWDADRMIHMFITGCSMGPPLHYWYLLLD

Parental  GAFPAAGLSGIRTVLKKVFIDQIVASPALGVWYFLGMGTLEGQALERSWQELEDNFWEFYKMDWCVWPPA
          ...P..G......V..KV.IDQ..A.P..G.WYF..MG.L.G..L..S..E....FWE.......VWP.A
Retrocopy KITPGKGMQHVKIVVLKVTIDQAFA-PFFGCWYFTWMGLLQGHSLADSLKEFKEKFWEYFIAELTVWPAA

Parental  QLVNFLFLPPKYRVVYMNVITLGWDTYLSYLKHR
          QLVNF.FL.PKYRV...N..TLGW..YLSYLKHR
Retrocopy QLVNFFFLQPKYRVIFVNMVTLGWNVYLSYLKHR

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	0.13 RPM	7.61 RPM
SRP009831_brain	0.19 RPM	6.58 RPM
SRP009831_dewlap	0.00 RPM	9.75 RPM
SRP009831_embryo	0.00 RPM	12.54 RPM
SRP009831_heart	0.21 RPM	5.71 RPM
SRP009831_liver	0.04 RPM	22.09 RPM
SRP009831_lung	0.00 RPM	8.61 RPM
SRP009831_ovary	0.00 RPM	10.15 RPM
SRP009831_skeletal_muscle	0.00 RPM	9.18 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_180 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_180 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000027644	1 retrocopy	retro_acar_180 ,
Bos taurus	ENSBTAG00000025788	1 retrocopy	retro_btau_306,
Callithrix jacchus	ENSCJAG00000014104	1 retrocopy	retro_cjac_4063,
Echinops telfairi	ENSETEG00000013840	1 retrocopy	retro_etel_1446,
Macropus eugenii	ENSMEUG00000016379	2 retrocopies	retro_meug_223, retro_meug_943,
Macaca mulatta	ENSMMUG00000005025	1 retrocopy	retro_mmul_2493,
Nomascus leucogenys	ENSNLEG00000005944	1 retrocopy	retro_nleu_2666,
Pteropus vampyrus	ENSPVAG00000002028	1 retrocopy	retro_pvam_1254,