RetrogeneDB ID: retro_acar_38

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:191348118..191348748(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000009816
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000015685
• Aliases: None
• Description: Synaptosomal-associated protein [Source:UniProtKB/TrEMBL;Acc:G1KRG6]

Sequence

>retro_acar_38
ATGGCTGAGTTATTGTCATCTGAAGAAATTCAACTGAAGATCCATCAGCTTAAAGATGAATCTTTAGAATGCTCTGAGAG
GATTTGTCTCTTGGCTTCTGAATGCCAAGATGCAGGGATCAAAATCATCTCTATGCTGGATGAACAAGGGGAACAGCTGA
ATCGTATAGAAGGAAGCATGGACCATATAGAGAAAGATGTGAAAGAAGCAGAGAAGAGCTTGATGGAGCTCAGCAAATGC
TGTGGCCTCAACGTCTGTCCTTCCAAGAACAGGAAGAAAGCAGGAAGGAAACCCTGCAAGACAATTTTGGATGATGAAGA
GGACTTAAACCACAATGTAGTATTTGAACAACCAAGGTATGTAACGCATCTGAAGAAGAAAGAATTATTGGAAGCAAGAA
GCAGAGGTTGCAAAGCACAGAAAGCAAATGATGCCAGAGATTGTAAGACAGAAGAGAATCTTACTCAAGTGGGAAACATA
TTGGGGAATCTGAAAAATATGGCATTGGAGATGGGCAATGTGCTTCATAAGCAAAACAAACAGGTCAACTGGATAAACAA
AAAAGCGGACATCAATACATCTCTTATTGAACAGGCCAACGCAAAGGCCAAAAATTGCATTGACTACTAA

Alignment

ORF - retro_acar_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEL-SPEDIQLRAHQVTDESLESTRRILGLAVESQDAGIKTISMLDEQGEQLNRIEEGMDQINKDMREA
          MAEL.S.E.IQL..HQ..DESLE...RI..LA.E.QDAGIK.ISMLDEQGEQLNRIE..MD.I.KD..EA
Retrocopy MAELLSSEEIQLKIHQLKDESLECSERICLLASECQDAGIKIISMLDEQGEQLNRIEGSMDHIEKDVKEA

Parental  EKNLKELNKCCGLCVCPCNRTKNFESSKSYRTTWGDGMENSGDHVVSKQP
          EK.L.EL.KCCGL.VCP....K..........T..D..E.....VV..QP
Retrocopy EKSLMELSKCCGLNVCPSKNRK--KAGRKPCKTILDDEEDLNHNVVFEQP

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	0.10 RPM	62.79 RPM
SRP009831_brain	0.24 RPM	14.58 RPM
SRP009831_dewlap	0.17 RPM	86.40 RPM
SRP009831_embryo	1.19 RPM	29.43 RPM
SRP009831_heart	0.10 RPM	54.74 RPM
SRP009831_liver	0.12 RPM	57.71 RPM
SRP009831_lung	0.25 RPM	87.95 RPM
SRP009831_ovary	0.04 RPM	86.79 RPM
SRP009831_skeletal_muscle	0.04 RPM	22.44 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_38 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_38 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38 ,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,