RetrogeneDB ID: retro_cfam_1404

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:16147107..16148841(+)
• 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_1404
TCTACCATAATAATCATTGGAGAAGCAGCAACACAGCCTCCCAATTCAGAATCAGAAAAAAAGAAGAAGAAAAAGAGAAA
AATGATGGATGACACTGGGCCTGATAAAAAAAAATCGAAAACAAGACGAAGGGGACTCTGAAGAAAGGACCCAGGCTCCT
GAAGAGACAGAAAACAATGTGGAGAAGCCAGATGATGAGGAGGAGGACAGTGAAGTGCCCAGCCTACTCCTGGGACTGAC
AGGAGCTTTTGAGGATACTTCATTTGCTTCTCTTTCTGATCTTGTCAATGAGAACACTCTGAAGGCAATAAAAGAATTGG
GTTTTACAAACATGACTGAAATTCAGCATAAAAGTATCAGACCACTTCTGGAAGACAGGGATCTCCTTGCGGCCGCAAAA
ACAGGCAGTGGCAAAACGCTGGCATTTCTCATTCCTGCAGTCGAACTCATTGTCAAGTTAAAAGTTCATGCCTAGGAATA
AACAGGAGTTCTTATCCTCTCACCTACTAGGGAACTGGCCATGCAGACTTTGGGTGTTCTTAAAGAGTTAATGACACACC
ATGTTCACACATACGGGTTAATAATGGGTGGCAGCAACAGATCTGCTGAAACACAGAAACTTGATAACAGGATCAACATC
ATTGTGGCCACACCAGGCGGTCTGCTGGGCCACATGCAGAATACCCCAGGTTTTATGTATAAAAATCTACAATGTCTGGT
TATTGATGAGGCTCATCGTATCTTGGATGTTGGGTTTGAAGAGGAATTAAAACAAATTATTAAACTTCTGCCAACACGCA
GGCAAACCATGCTCTTTTCTGCCACACAAATTCGAAAAGTTGAAGACTTGGCAAGGATTTCTTTGAAAAAGGAGCCATTG
TATGTTGGTGTTGATGAAGATAAAGCTAATGCGACAGTGGATGGTCTTGAGCAGGGATATGTTGCTTGTCCCTCAGAAAA
GAGGTTCCTTCTGTTCTTTACATTCCTTAAGAAGAACCGGAAGAAGAAAGTGATGGTCTTCTTTTCATCCTGTAAGTCCA
TGAAATACCACTATGAGTTGCTGAACTACATCGATTTGCCTGTCTTGGCCATTCATGGAAGGCAGAGGCAAAATAAGCGT
ACAACCACATTCTTCCAGTTCTGCAATGCTGATTCGGGGATATTGTTGTGTACAGACATGGCAGCTAGAGGGCTAGATAT
TCCTGAAGTCGATTGGATTGTTCAGTATGACCCTCCAGGTGACCCCAAGGAATATATTCGTGTGGGAAGGACAGCCAGAG
GCCTAAACGGAAGAGGTCACGCCTTGCTCATCTTACGCCCTGAAGAGTTGGGTTTCCTTCCTTACTTGAAGCAATCCAAG
GTTCCATTAAGTGAATTTGAGTTTTCCTGCTCCAAGATTTCTGACATTCAGTCTCAGCTTGAAAAACTGATTTAAAAGAA
CTACTTCCTTCATAAGTCAGTGCAGAAGGCATATAAGTCCTACATTTGAGCATATGATTCCCATTCTCTGAAACAGATCT
TCAATTTAATAACTTAAATTTGCCTCAAGTTGCTCTGTCCTTTGGTTTCAAGGTGCCTCCTTTTGTTGATCTGAACGTGA
ACAGCAATGATGGCAAGCTTAAAAAGAGAGGAGGTGGCGGCAGCTTTGCATACCAGAAAGCCAAGAAAGTTGAGAAGTAC
AAAATCTTCAAACACATTAGCAGGAAGTCCTCTGACAGCCGGCAGTTCTCCCAC

Alignment

ORF - retro_cfam_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 86.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  STIIVNGEAETQPPNSESKKKKKRKRKMVDDAGPDTKKSKT-EDKG-DSEEGTQAPEETENNGEKPDDEE
          STII..GEA.TQPPNSE............DD.GPD...SKT...KG.DSEE.TQAPEETENN.EKPDDEE
Retrocopy STIIIIGEAATQPPNSEXXXXXXXXXXXMDDTGPDXXXSKT<KTKG<DSEERTQAPEETENNVEKPDDEE

Parental  EDSEVPSLPLGLTGAFEDTSFASLSSLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSG
          EDSEVPSL.LGLTGAFEDTSFASLS.LVNENTLKAIKE.GFTNMTEIQHKSIRPLLE.RDLLAAAKTGSG
Retrocopy EDSEVPSLLLGLTGAFEDTSFASLSDLVNENTLKAIKELGFTNMTEIQHKSIRPLLEDRDLLAAAKTGSG

Parental  KTLAFLIPAVELIVKL-KFMPRNG-TGVLILSPTRELAMQTFGVLKELMMYHVHTYGLIMGGSNRSAEAQ
          KTLAFLIPAVELIVKL.KFMPRN..TGVLILSPTRELAMQT.GVLKELM..HVHTYGLIMGGSNRSAE.Q
Retrocopy KTLAFLIPAVELIVKL>KFMPRNK<TGVLILSPTRELAMQTLGVLKELMTHHVHTYGLIMGGSNRSAETQ

Parental  KLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSAT
          KL.N.INIIVATPG.LL.HMQNTPGFMYKNLQCLVIDEA.RILDVGFEEELKQIIKLLPTRRQTMLFSAT
Retrocopy KLDNRINIIVATPGGLLGHMQNTPGFMYKNLQCLVIDEAHRILDVGFEEELKQIIKLLPTRRQTMLFSAT

Parental  QTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCK
          Q.RKVEDLARISLKKEPLYVGVD.DKANATVDGLEQGYV.CPSEKRFLL.FTFLKKNRKKK.MVFFSSCK
Retrocopy QIRKVEDLARISLKKEPLYVGVDEDKANATVDGLEQGYVACPSEKRFLLFFTFLKKNRKKKVMVFFSSCK

Parental  SVKYHYELLNYIDLPVLAIHGRQKQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDP
          S.KYHYELLNYIDLPVLAIHGRQ.QNKRTTTFFQFCNADSGILLCTD.AARGLDIPEVDWIVQYDPP.DP
Retrocopy SMKYHYELLNYIDLPVLAIHGRQRQNKRTTTFFQFCNADSGILLCTDMAARGLDIPEVDWIVQYDPPGDP

Parental  KEYIHRVGRTARGLNGRGHALLILHPEELGFLRYLKQSKVPLSEFEFSWSKISDIQSQLEKLIEKNYFLH
          KEYI.RVGRTARGLNGRGHALLIL.PEELGFL.YLKQSKVPLSEFEFS.SKISDIQSQLEKLI.KNYFLH
Retrocopy KEYI-RVGRTARGLNGRGHALLILRPEELGFLPYLKQSKVPLSEFEFSCSKISDIQSQLEKLI*KNYFLH

Parental  KSAQEAYKSYIRAYDSHSLKQIFNV-NNLNLPQVALSFGFKVPPFVDLNVNSNDGKLKKRGGGGGFGYQK
          KS.Q.AYKSYI.AYDSHSLKQIFN..NNLNLPQVALSFGFKVPPFVDLNVNSNDGKLKKRGGGG.F.YQK
Retrocopy KSVQKAYKSYI*AYDSHSLKQIFNL<NNLNLPQVALSFGFKVPPFVDLNVNSNDGKLKKRGGGGSFAYQK

Parental  AKKVEKSKIFKHISRKSSDSRQFSH
          AKKVEK.KIFKHISRKSSDSRQFSH
Retrocopy AKKVEKYKIFKHISRKSSDSRQFSH

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	0.53 RPM	31.57 RPM
SRP017611_liver	0.73 RPM	12.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1404 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1404 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,