RetrogeneDB ID: retro_cfam_1864

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:75323093..75323606(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018694
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NECAP2
• Ensembl ID: ENSCAFG00000015895
• Aliases: None
• Description: NECAP endocytosis associated 2 [Source:HGNC Symbol;Acc:25528]

Sequence

>retro_cfam_1864
CACCGTGGCTACAGGGCCGCGGAGTGGCAGCTGGACCAGCCATCACGGAGTGGCCGGCTGCGGATCACTGCAAAAGGGCG
GGTGGCCTTCATCAAGCTGGAGGACGGGACCTCAGGGGAGCTCTTTGCTCAGGCCCCGGTGGACCAGTTTCCTGGCCCAG
CCGCGGAGAGCGTGACCCATTCCAGCAGATACTCTGTTATCCGCATCGAAGATGGAAATGGACCCCGGGCATTTGTTGGA
ATTGGCTTCGGGGACCGAGGCGACGCCTTTGACTTCAATGTTGCGTTGCAGGACCATGCCGAGTGGGTGAAACAGCAAGC
AGTGTGAATTTGCAAAACAAGCCCAGACCCCAGACCAGGGCCCCAAGTTGGACCTCGGCTTCCAAGAGGGCCAGACCAAG
CTCAACATCGCGAACATGAAGAAGAAGGAAGGAGCAGGAGGACTGAGCCTGCTTCCCCGCGCCCAGGGGGGAAAACCTCT
ACCCTGATCCCTCCCCCCGGGGAGCAGTTGTCT

Alignment

ORF - retro_cfam_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 64.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NRGYRAAEWQLDQPSWSGRLRITAKGQVAYIKLEDRTSGELFAQAPVDQFPGTAVESVTDSSRYFVIRIE
          .RGYRAAEWQLDQPS.SGRLRITAKG.VA.IKLED.TSGELFAQAPVDQFPG.A.ESVT.SSRY.VIRIE
Retrocopy HRGYRAAEWQLDQPSRSGRLRITAKGRVAFIKLEDGTSGELFAQAPVDQFPGPAAESVTHSSRYSVIRIE

Parental  DGNGRRAFIGIGFGDRGDAFDFNVALQDHFKWVKQQCE-FAKQAQNP-DQGPKLDLGFKEGQTIKLNIAN
          DGNG.RAF.GIGFGDRGDAFDFNVALQDH..WVKQQ.....K....P.DQGPKLDLGF.EGQT.KLNIAN
Retrocopy DGNGPRAFVGIGFGDRGDAFDFNVALQDHAEWVKQQAV*ICKTSPDP>DQGPKLDLGFQEGQT-KLNIAN

Parental  MKKKEGAAG-TPRARPASTGGLSLLPPPPGGKTS
          MKKKEGA.G.T..A.P...G..S.L.PPPG...S
Retrocopy MKKKEGAGG<TEPASPRPGGKTSTLIPPPGEQLS

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	20.54 RPM
SRP017611_brain	0.00 RPM	8.97 RPM
SRP017611_kidney	0.00 RPM	23.31 RPM
SRP017611_liver	0.00 RPM	8.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1864 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1864 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Canis familiaris	ENSCAFG00000015895	1 retrocopy	retro_cfam_1864 ,
Callithrix jacchus	ENSCJAG00000008146	2 retrocopies	retro_cjac_1447, retro_cjac_2449,
Macropus eugenii	ENSMEUG00000006140	1 retrocopy	retro_meug_2149,