RetrogeneDB ID: retro_cfam_2116

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:98206052..98207317(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSCAFG00000004950
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_cfam_2116
GTGGATGACACTGGGCCTGATACCAAAAAATCGAAAACTGAAGACAAAGGGGACTCTGAAGAAGGGGCCGAGGCTCCTGA
AGAGACAGAAAACATTGCAGAGAAGCCAGATGATGAGGAAGAGGACAGTGAACTGCCCAGAGTATCCCTGGGACTGACAG
GAGCTTTTGAGGATACTTTATTTGCTTCTCTTTCTAATCTTGTCAATGAGAACACTCTGAAGGCAATGAAAGAAATGGGT
TTTACAAACATGATTGAAATTCAGCATAAAAGTATCAGACCACTGCTGGAAGGCAGGGATCTCCTAGCAGCTGCAAAAAC
AGGCAGTGGCAAAATGCTGGCATTTCTCATCCCTGTAGTCCAACTCATTGGCATGTTAAAGTTCATGCCTAGGAATGGAA
CAGGACTTCTTATTCTCTCATCTACTAGGGAACTGGCCATGCAGACTTTTGGTGTTCTTAAAGAGCTAATGATACACTAT
GTTCGCACATACAGGTTAATAATGGATGGCAGCAACAGATCTGCTGAAGCACAGAAACTTGGTAATGGGATCAACATCAT
TGTGGCCACCCCAAGCCATCTCCTGGACCACATGCAGAATACCCCAGGGTTTATGTATAAAAATCTACATTATGTGGTTA
TCGATGAGGCTGATCATGTCTTGGATGTTGGGTTTGAAGACAAATTAAAATAAATTATTAAACTTCTGCCAGCACACAGG
CAAACCATGCTCTTTTCTGCCACACAAACTCAAAAAGTTGAGACTTGTCAAGGATTTCTTTGAAAAAGGAACCATTGTAT
GTTGGTATTGATGACGATAAAGCTAATGCAACAGCGGATGGTCTTGAACAGGGATGTGTTGTTTGTCCCTCAGAAAAGAG
GTTCCTTCTGCTCTTTACATCCTTAAGAAGAACCAGAAGAAGAAACTGATGGTCTTCTTTTCATCCTGTAAGTCCGTGAA
ATACCACTATGAGTTGCTGAACTACATTGATTTGCCTGTCTTGGCCATTCATGGAAGGCAGAAGCAGAATAAGCATACAA
CCACATTCTTCCAGTTCTGCAATGCTGATTGGGGGATATTGTTGTGTAAAGACATGGCAGCTAGAGGGCTGGATATTCCT
GAAGTCGATTGGATTGTTCAGTATGACTTTCCAAATGATCCCAAGGAATATATTCATCATGTGGGAACAGCCAGAGGCCT
AAACAGAAGAGGTCACGCCTTGCTCATCTTACCCTGAAGAGTTGGGTTTCCTTTGTTACTTGAAG

Alignment

ORF - retro_cfam_2116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 63.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDDAGPDTKKSKTEDKGDSEEGTQAPEETENNGEKPDDEEEDSEVPSLPLGLTGAFEDTSFASLSSLVNE
          VDD.GPDTKKSKTEDKGDSEEG..APEETEN..EKPDDEEEDSE.P...LGLTGAFEDT.FASLS.LVNE
Retrocopy VDDTGPDTKKSKTEDKGDSEEGAEAPEETENIAEKPDDEEEDSELPRVSLGLTGAFEDTLFASLSNLVNE

Parental  NTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNGTGVLILS
          NTLKA.KEMGFTNM.EIQHKSIRPLLEGRDLLAAAKTGSGK.LAFLIP.V.LI..LKFMPRNGTG.LILS
Retrocopy NTLKAMKEMGFTNMIEIQHKSIRPLLEGRDLLAAAKTGSGKMLAFLIPVVQLIGMLKFMPRNGTGLLILS

Parental  PTRELAMQTFGVLKELMMYHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQ
          .TRELAMQTFGVLKELM...V.TY.LIM.GSNRSAEAQKLGNGINIIVATP..LLDHMQNTPGFMYKNL.
Retrocopy STRELAMQTFGVLKELMIHYVRTYRLIMDGSNRSAEAQKLGNGINIIVATPSHLLDHMQNTPGFMYKNLH

Parental  CLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE-DLARISLKKEPLYVGVDDDKANATV
          ..VIDEAD..LDVGFE..LK.IIKLLP..RQTMLFSATQT.KVE.DL.RISLKKEPLYVG.DDDKANAT.
Retrocopy YVVIDEADHVLDVGFEDKLK*IIKLLPAHRQTMLFSATQTQKVE<DLSRISLKKEPLYVGIDDDKANATA

Parental  DGLEQGYVVCPSEKRFLLLFT-FLKKNRKKKLMVFFSSCKSVKYHYELLNYIDLPVLAIHGRQKQNKRTT
          DGLEQG.VVCPSEKRFLLLFT..LKKN.KKKLMVFFSSCKSVKYHYELLNYIDLPVLAIHGRQKQNK.TT
Retrocopy DGLEQGCVVCPSEKRFLLLFT<ILKKNQKKKLMVFFSSCKSVKYHYELLNYIDLPVLAIHGRQKQNKHTT

Parental  TFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILHPEELG
          TFFQFCNAD.GILLC.D.AARGLDIPEVDWIVQYD.P.DPKEYIH.VG.TARGLN.RGHALLIL.P...G
Retrocopy TFFQFCNADWGILLCKDMAARGLDIPEVDWIVQYDFPNDPKEYIHHVG-TARGLNRRGHALLIL-P*RVG

Parental  -FLRYLK
          .FL.YLK
Retrocopy >FLCYLK

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	48.68 RPM
SRP017611_brain	0.00 RPM	40.73 RPM
SRP017611_kidney	0.00 RPM	31.57 RPM
SRP017611_liver	0.00 RPM	12.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2116 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116 ,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,