RetrogeneDB ID: retro_acar_197

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343634.1:169551..169876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSACAG00000013718
• Aliases: None
• Description: None

Sequence

>retro_acar_197
AGAGACAGGGGCTTTAGCTTAATCATCTTAACCAGTCATGAGCATGCATTAAATGCCATGATAGTCATGAATGGTGGGTA
TATAGAAGGATGCCATATCAGAGTTGACCATGCCGAAAAATCTTCCCATAGACCTAGAAGTGGATATTTTGGAGGCAGAG
GGTATGGCTGTGGATATTCCCAATCTAGTAGAGACAAACGCTATGGTGGATGCTAATGAAAACCAAAGTGGAGGTTACTG
TGATTTCTGGGACTATGGAGGAAGTCAGGAAGTGTATAATGACCACTATTCCTCAGACGTCTCTTACAGAAACAACTATG
ACAAT

Alignment

ORF - retro_acar_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.88 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSRGFGFITFANPEHASDAMRAMNGESVDGRQIRVDHAGKSSRGSRGGYFGGRGRGRGYSRGGGDRSYGG
          R.RGF..I.....EHA..AM..MNG....G..IRVDHA.KSS...R.GYFGGRG.G.GYS....D..YGG
Retrocopy RDRGFSLIILTSHEHALNAMIVMNGGYIEGCHIRVDHAEKSSHRPRSGYFGGRGYGCGYSQSSRDKRYGG

Parental  -RYDNRSGGYGGSRDYGRSQGGYNDRYSSGGSYRDNYDN
          ....N.SGGY....DYG.SQ..YND.YSS..SYR.NYDN
Retrocopy >ANENQSGGYCDFWDYGGSQEVYNDHYSSDVSYRNNYDN

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	930.50 RPM
SRP009831_brain	0.00 RPM	221.60 RPM
SRP009831_dewlap	0.00 RPM	508.73 RPM
SRP009831_embryo	0.03 RPM	1829.39 RPM
SRP009831_heart	0.00 RPM	332.77 RPM
SRP009831_liver	0.00 RPM	516.06 RPM
SRP009831_lung	0.00 RPM	436.93 RPM
SRP009831_ovary	0.04 RPM	507.43 RPM
SRP009831_skeletal_muscle	0.00 RPM	205.49 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_197 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_197 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 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197 ,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,