RetrogeneDB ID: retro_cfam_1112

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:49363787..49364429(+)
• Located in intron of: ENSCAFG00000008746

Retrocopy information

• Ensembl ID: ENSCAFG00000008758
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1112
ACCGAGGCTGTGCTGAAGGGCAAGGGCCTCGGCACCGGCACGCTCTGCACCGCGGAGAGCCGCCTGTCTTGGTTAGATGG
CTCTGGATTAGGATTCTCACTGGAATACCCCACCATTAGCTTGCATGAGGTGTCCAGGGACCTAAATGCCTATCCACGAG
AGCATTTGCATGTTATGGTGAATGCTAAATTTGGAGAAGAATCAAAAGAATCTGTTGCTGAAGAAGAAGAAGACAGTGAT
GATGATGTTGAACCTATTGCTGAATTTAGATTTGTGCCTAGTGATAAATCAGCATTGGAGGCAATGTTCACTGCAATGTG
TGAATGCCAGGCTTTGCATCCTGATCCTGAGGATGAAGATTCAGATGATTACGATGGAGAAGAATATGATGTGGAAGCAC
ATGAACAAGGGCAGGGGGACATCCCTACATTTTATACCTATGAAGAAGGATTATCCCATTTAACAGCAGAAGGCCAGGCC
ACCTTGGAGAGATTAGAAGGAATGCTTTCTCAGTCTGTGAGCAGCCAATATAACATGGCTGGAGTCCGGACAGAAGATTC
AATCAGAGATTATGAAGATGGGATGGAGGTAGACACTACACCAACAGTTGCTGGACAGTTTGAGGATGCAGATGTTGATC
AC

Alignment

ORF - retro_cfam_1112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.2 %
• Parental protein coverage: 90.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHAVSRDLNAYPREHLYVMVNAKFGEESKE
          TEAVL.GKGLGTGTL..AESRLSWLDGSGLGFSLEYPTISLH.VSRDLNAYPREHL.VMVNAKFGEESKE
Retrocopy TEAVLKGKGLGTGTLCTAESRLSWLDGSGLGFSLEYPTISLHEVSRDLNAYPREHLHVMVNAKFGEESKE

Parental  SVA-EEEDSDDDVEPIAEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQGD
          SVA.EEEDSDDDVEPIAEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQGD
Retrocopy SVAEEEEDSDDDVEPIAEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQGD

Parental  IPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSIRDYEDGMEVDTTPTVAGQFEDA
          IPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSIRDYEDGMEVDTTPTVAGQFEDA
Retrocopy IPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSIRDYEDGMEVDTTPTVAGQFEDA

Parental  DVDH
          DVDH
Retrocopy DVDH

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	22.51 RPM
SRP017611_brain	0.00 RPM	12.54 RPM
SRP017611_kidney	0.00 RPM	14.66 RPM
SRP017611_liver	0.00 RPM	3.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1112 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1112 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,