RetrogeneDB ID: retro_cfam_1176

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:7222400..7222930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL1
• Ensembl ID: ENSCAFG00000006992
• Aliases: None
• Description: ADP-ribosylation factor-like 1 [Source:HGNC Symbol;Acc:692]

Sequence

>retro_cfam_1176
ATGGGTGGCTTTTTATCAAATATTTTGTCTAGTCTTGTTTGGAACCCCAAGAAATGAGGATTTTAATTTTGAGATTGTAT
GGAGCAGGAAAAATGTAATTTTGTACAGATTGCAGGTTGGAGAAGTGGTTACTACTATTCCTACCATCGGATTTAATGTT
GGGACAGTAATATATGAGAACCTTAAATCCCAAGTCTGGGATTGAGGAGGACAGACAAGGCTCATGCCATACTGGAGATG
TCATTATTCAAACACGGATACAGTCGTTTCTATAGTAGACAGTTGTGACCGAACCAAACTGGCATTCCCACGTCAGAGTT
AGTGGCTATGCTGGAGAAAGAAGAGCTGAGAAAAGCCATTTTGGTGGTGTTTACAAATAAGCAGGGCATGCAGCAGGCCG
TGACTCCATTAGAGATGCCAATTCTCTTGAGTTACCAGCACTGAAGGACCCACAGCGACAGATATGCAAACCTTCAGCAA
CCCAAGTCACTGGCTTCAATGAGGCAATGAGATGGTTAGCTGGAACATTA

Alignment

ORF - retro_cfam_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.53 %
• Parental protein coverage: 97.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGGFFSSIFSSL-FGT-REMRILILGLDGAGK-TTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWD
          MGGF.S.I.SSL.FGT..EMRILIL.L.GAGK...ILYRLQVGEVVTTIPTIGFNV.TV.Y.NLK.QVWD
Retrocopy MGGFLSNILSSL>FGT>QEMRILILRLYGAGK<NVILYRLQVGEVVTTIPTIGFNVGTVIYENLKSQVWD

Parental  LGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRI-GISKSELVAMLEEEELRKAILVVFANKQDMEQAMTP
          .GGQT...PYWRC.YSNTD.V...VDSCDR....GI..SELVAMLE.EELRKAILVVF.NKQ.M.QA.TP
Retrocopy *GGQTRLMPYWRCHYSNTDTVVSIVDSCDRTKL<GIPTSELVAMLEKEELRKAILVVFTNKQGMQQAVTP

Parental  SEM-ANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL
          .EM.ANSL.LPALKD...QI.K.SAT..TG..EAM.WL..TL
Retrocopy LEM<ANSLELPALKDPQRQICKPSATQVTGFNEAMRWLAGTL

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
SRP012049_cerebellum	0.00 RPM	27.09 RPM
SRP017611_brain	0.00 RPM	27.07 RPM
SRP017611_kidney	0.07 RPM	47.81 RPM
SRP017611_liver	0.00 RPM	11.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1176 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016452	2 retrocopies	retro_amel_1138, retro_amel_713,
Canis familiaris	ENSCAFG00000006992	2 retrocopies	retro_cfam_1176 , retro_cfam_709,
Callithrix jacchus	ENSCJAG00000001966	1 retrocopy	retro_cjac_2938,
Echinops telfairi	ENSETEG00000020310	1 retrocopy	retro_etel_1850,
Macropus eugenii	ENSMEUG00000015525	1 retrocopy	retro_meug_518,
Myotis lucifugus	ENSMLUG00000002351	1 retrocopy	retro_mluc_255,
Monodelphis domestica	ENSMODG00000003056	1 retrocopy	retro_mdom_677,
Mustela putorius furo	ENSMPUG00000011822	1 retrocopy	retro_mputfur_1458,
Mus musculus	ENSMUSG00000060904	1 retrocopy	retro_mmus_3285,
Oryctolagus cuniculus	ENSOCUG00000002217	5 retrocopies	retro_ocun_1608, retro_ocun_399, retro_ocun_400, retro_ocun_465, retro_ocun_847,
Otolemur garnettii	ENSOGAG00000015144	1 retrocopy	retro_ogar_1239,
Pteropus vampyrus	ENSPVAG00000008119	2 retrocopies	retro_pvam_1072, retro_pvam_715,
Rattus norvegicus	ENSRNOG00000005763	1 retrocopy	retro_rnor_2375,
Sorex araneus	ENSSARG00000013944	4 retrocopies	retro_sara_237, retro_sara_304, retro_sara_479, retro_sara_71,
Sarcophilus harrisii	ENSSHAG00000004634	2 retrocopies	retro_shar_204, retro_shar_275,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000, retro_itri_348,
Tarsius syrichta	ENSTSYG00000013257	5 retrocopies	retro_tsyr_1803, retro_tsyr_188, retro_tsyr_350, retro_tsyr_369, retro_tsyr_809,
Tursiops truncatus	ENSTTRG00000017202	1 retrocopy	retro_ttru_701,