RetrogeneDB ID: retro_cfam_981

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:17010509..17010866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSCAFG00000006039
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_cfam_981
ATGATTCTGTCTTCTACCAACCTGGTTACTGGAATCCCCAGTAGTAAAGTAAAATTTTCAAGGCTTTCCAGCACAGATGA
TGACTACATTGACCTTGAGTTTAAGAAAAACATTCATGGGGTCACATATGAGGTATAGTACTATTTTTGATTGACGTCTT
TCTCATCATAGGCTGCCTCCTGCTAGCTGGCTATCTCAAAAAAGGGTGGTGGGCGGTAGGGGCAGACCAGGGTCCTTCAG
TCCTGATCACTGGCATCCTGGTGTTCCTGCCAGAATTGTACCACCTGCATATCTCCTACTATGCATCCAAAGGCTACTGG
GGTTACTCCTACCAATGACATTCCAGATTTTGATGAC

Alignment

ORF - retro_cfam_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYK-AIALATV-LFLIGAFLIIIGSLLLA
          M..S.TNL.TGIPSSKVK.SRLSSTDD.YIDL.FKK......Y...I.L.....FLI...L...G..L..
Retrocopy MILSSTNLVTGIPSSKVKFSRLSSTDDDYIDLEFKKNIHGVTYE<GIVLFLIDVFLIIGCLLLAG-YLKK

Parental  GYISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSY-DDIPDFDD
          G....G.AD....VLI.GILVFLP..YHL.I.YYASKGY.GYSY..DIPDFDD
Retrocopy GWWAVG-ADQGPSVLITGILVFLPELYHLHISYYASKGYWGYSY>NDIPDFDD

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	16.84 RPM
SRP017611_brain	0.00 RPM	12.86 RPM
SRP017611_kidney	0.00 RPM	25.62 RPM
SRP017611_liver	0.00 RPM	15.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_981 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Canis familiaris	ENSCAFG00000006039	1 retrocopy	retro_cfam_981 ,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373, retro_dnov_803,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502,
Pteropus vampyrus	ENSPVAG00000002863	1 retrocopy	retro_pvam_44,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,