RetrogeneDB ID: retro_cfam_481

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:23712514..23713258(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003053
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC1
• Ensembl ID: ENSCAFG00000000621
• Aliases: None
• Description: Canis lupus familiaris chloride intracellular channel 1 (CLIC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252138]

Sequence

>retro_cfam_481
CGCTTCCTGGTCCCCGTCGCAACCATGGCTGAAGAACCACCTCAGGTTGAACTGTTCGTGACGGCCGGCAGTGATGGGGC
CAAGATTGGGAACTGCCCCTTCTCCCAGAGACTGTTCATGGTACTCTGGCTCAAAGGAGTCACCTTCAACGTAACCACTG
TTGACACCAAGAGGCGGACCGAGACGGTACAGAAGCTGTGCCCAGGAGGGCAGCTCCCTTTCCTTCCCTACCGCACTGAA
GTGCACACAGACACCAACAACATTGAGGAGGTTCTGGAGGCAGTGCTGTGCCCTCCCAGGTACCCCAAGCTGGCAGCTCT
GAACCCTGAATCCAACACGGCTGGGCTGGACATATTTGCCAAATTTTCTGCTTACATCAAGAATTCAAACCCGGCACTCA
AGGATAATCTGGAGAAGGGGCTCCTGAAAGTCTTGAAAGTTTTAGACAATTACTTGACATCCCCCCTCCCAGAAGAAGGG
GATGAGACCAGTGCTGAGAATGAGGGCATCTCGCAGAGGAAGTTTCTGGATGGCAATGAGCTCACTCTGGCTGACTGCAA
CCTCTTGCCAAAACTCCACATAGTACAGGTGGTGTGTAAGAAATACAGGGGATTCTCCATCCCAGAGGTGTTCCGCGGGG
TGCATCGGTACTTGCATAATGCCTATGCTCGGGAAGAGTTTGCCTCCACCTGTCCAGATGATGAGGAGATCGAGCTGGCT
TATGAGCAAGTGGCCAAGGCCCTC

Alignment

ORF - retro_cfam_481 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFLVPVATMAEEQPQVELFVKAGSDGAKIGNCPFSQRLFMVLWLKGVTFNVTTVDTKRRTETVQKLCPGG
          RFLVPVATMAEE.PQVELFV.AGSDGAKIGNCPFSQRLFMVLWLKGVTFNVTTVDTKRRTETVQKLCPGG
Retrocopy RFLVPVATMAEEPPQVELFVTAGSDGAKIGNCPFSQRLFMVLWLKGVTFNVTTVDTKRRTETVQKLCPGG

Parental  QLPFLLYGTEVHTDTNKIEEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALNDNLEKG
          QLPFL.Y.TEVHTDTN.IEE.LEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPAL.DNLEKG
Retrocopy QLPFLPYRTEVHTDTNNIEEVLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALKDNLEKG

Parental  LLKALKVLDNYLTSPLPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFSIPEV
          LLK.LKVLDNYLTSPLPEE.DETSAE.EGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFSIPEV
Retrocopy LLKVLKVLDNYLTSPLPEEGDETSAENEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFSIPEV

Parental  FRGVHRYLRNAYAREEFASTCPDDEEIELAYEQVAKAL
          FRGVHRYL.NAYAREEFASTCPDDEEIELAYEQVAKAL
Retrocopy FRGVHRYLHNAYAREEFASTCPDDEEIELAYEQVAKAL

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	19.45 RPM
SRP017611_brain	0.00 RPM	8.34 RPM
SRP017611_kidney	0.00 RPM	60.62 RPM
SRP017611_liver	0.00 RPM	11.53 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_481 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_481 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481 , retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506, retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,