RetrogeneDB ID: retro_cfam_255

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:35055184..35055884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSCAFG00000004900
• Aliases: CLNS1A, ICLN
• Description: Canis lupus familiaris chloride channel, nucleotide-sensitive, 1A (CLNS1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001003288]

Sequence

>retro_cfam_255
ATGAGCTTCCTTAAAAGTTTCCTGCAGCCTGGGTTGGCTGGGGGGCTTTAGCAGCAGCAATTGGGTCCTACAGTTATGCT
GCACAGGCAGGACCTCTGCGCCAGCACCCTCTATATGCCCAAAGCTGCATGTCCTGGTTAGTCAGCTCTGGATGAGGGTT
CTTAGTAGAATACTCCACCATGAGTTTGCATGCGGTATCCAGGGACCTAAATGCCTGTCCACAAGAGTATTTGTGTGTTA
GGGTAAATGCCACATTTGGAGAAGATTTTTAGAAATCTGCTGCTGATGAAAAGGAAGACAGTGATGAGGGCCTTGAACCT
ATTGGTAAATTTAGATTTTTTCCTCACAATAAACCAGCACCGCGGGCAGCATTTACTGCAGTGTATGAATGCCAGGCTTT
GCGTCCAGATCTGTGGACAAAGAATCAGATGACTATGATAAAGAAGTATAGAATGTAGAAGCACAGGAACAGGGGCAGGG
GACATCCCTACATTTTATACATGAAGGATTATCCCATTTAACAATGGAAAGCCAAGCCACATTGGAGAGATGAGAAGGAA
GGCTTTCTCCATCTGTGGGCGGCCAACATAACATGGCTGGAGTGTGGACAAAAGATACAGTAAGAGATAAAGAAGATTGG
ATGGAAGTGGATACTATATCAACAGTTGCCGGCAAGTTTGAAGATGCAGATGTTGATCAC

Alignment

ORF - retro_cfam_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFLKSFPPPGSAEGLRQQQPETEAVLNGKGLGTGTLYI-AESRLSWLDGSGLGFSLEYPTISLHAVSRD
          MSFLKSF..PG.A.GL.QQQ......L....L...TLY..A.S..SWL..SG.GF..EY.T.SLHAVSRD
Retrocopy MSFLKSFLQPGLAGGL*QQQLGPTVMLHRQDLCASTLYM<AQSCMSWLVSSG*GFLVEYSTMSLHAVSRD

Parental  LNAYPREHLYVMVNAKFGEESKESVAEE-EDSDDDVEPIAEFRFVPSDKSALEAMFTAMCECQALHPD-P
          LNA.P.E.L.V.VNA.FGE....S.A.E.EDSD...EPI..FRF.P..K.A..A.FTA..ECQAL.PD..
Retrocopy LNACPQEYLCVRVNATFGEDF*KSAADEKEDSDEGLEPIGKFRFFPHNKPAPRAAFTAVYECQALRPD<S

Parental  EDEDSDDYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTED
          .D..SDDYD.E...VEA.EQGQG.........EGLSHLT.E.QATLER.EG.LS.SV..Q.NMAGV.T.D
Retrocopy VDKESDDYDKEV*NVEAQEQGQGT--SLHFIHEGLSHLTMESQATLER*EGRLSPSVGGQHNMAGVWTKD

Parental  SIRDYEDGMEVDTTPTVAGQFEDADVDH
          ..RD.ED.MEVDT..TVAG.FEDADVDH
Retrocopy TVRDKEDWMEVDTISTVAGKFEDADVDH

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	0.08 RPM	22.51 RPM
SRP017611_brain	0.08 RPM	12.54 RPM
SRP017611_kidney	0.26 RPM	14.66 RPM
SRP017611_liver	0.15 RPM	3.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_255 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_255 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255 , retro_cfam_327, retro_cfam_720, retro_cfam_727,
Choloepus hoffmanni	ENSCHOG00000007254	1 retrocopy	retro_chof_1685,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Dasypus novemcinctus	ENSDNOG00000008188	1 retrocopy	retro_dnov_477,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Myotis lucifugus	ENSMLUG00000024623	2 retrocopies	retro_mluc_1501, retro_mluc_1507,
Mustela putorius furo	ENSMPUG00000015944	1 retrocopy	retro_mputfur_435,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319, retro_itri_490,
Tupaia belangeri	ENSTBEG00000001316	1 retrocopy	retro_tbel_2975,