RetrogeneDB ID: retro_cfam_354

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:32862460..32863620(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000001943
• Aliases: CBWD2, CBWD1
• Description: None

Sequence

>retro_cfam_354
GTCAGAGCTGTGGATGAGGAAGAGGAGCAGACAGAGGAGGACTGTCCTGAATTGATCCCCATTGAGATGAGGGAAGGAGA
GGAGGAGGAAAAGTCTGGTCCTGGTACCAAGATCCTAGTCACAATTATCACTAGGTATTAAGGGGCTAGGTGCACCAATA
CTTCTGAAAAATATCTTGATGGAGCAACATAAGAAAAGAGTAGTAGTTATTTCAAACAAATTTGGGGGAGAAAGTACAGT
GGAGAAATCCTTATCTGTCAGCCAAAGTGAAGTTCTCTACCAAAAATAGTTGGAACTTAGAAATGATTGCCTCTGCTATT
CTACTGAATAGGATAGTGGCCCTGGAGCTAACGAGAATGTGATGCAGAAGAAGGGAAAATTTGATGACATACCATTAAAG
ACCACTGGATTAGCAGATGCTGGTGCTGTAGCATCTTTGTTTTGGGGTTGATGCTGAATTAGGGATTAATATTTCTCTTA
TTAGTATCAGAACTCTTGTGGATACAAAATATGGATTAAAACATTTAGCAGTAGAAAAACTCGATGGTCTTATCCAGGAG
GCTTCTAGGCAAACTGCTTCAGCAGATACCATTATCATTAATAAAACAGATTGGGTTTCACAAGAGGATTTAAACAAATT
AAGAATCACCATTAGATCAATAAATGGACTGGGAAAATTTTTAGAAACACAAGGATCAAGAGCTGATCTCTCTAATATAC
TAGCTCTTCATGTCTTTGACAGTCTCTCTGGAATATATTTGCAGAAAAACTTCAACACTTACCAACCACACAGCCTTGCG
CTGATCAGAGCATCATCAACATCACATTTTAGAACCAAGCGATGTGAAGGAAGAAAGTCTAAATGGATTTATTCAGAATC
TTCTGTGGGTGAAGAATGTGAGAAGCAAGGACAATGACTGCATGCAGGTCAAGCAACTCAAGGGGCAGGTGTTGATCAAA
GACAAACCAAAACCAATGATTGTCCAAGGTGCCCATGAGCTCTATGATCTGGAGGAGAGCTGGAAAGAAGATACTGAGAG
AACGAATCAATTGGCTCTTATTGATGGGAATCTAGATGAGGACATCTTCAATAACTACTTATAGCTACTAAGACTGAAAC
AGAAAAGTGGTGGACAACACATTTCAAAGAAGATCAAGTT

Alignment

ORF - retro_cfam_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.62 %
• Parental protein coverage: 98.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VGAVDEEEEPAEEDCPELVPIETKLREEEEKSGPGAKIPVTIITGYLGA-GKTTLLNYILTEQHSKRVAV
          V.AVDEEEE..EEDCPEL.PIE....EEEEKSGPG.KI.VTIIT.Y.GA.G...LL..IL.EQH.KRV.V
Retrocopy VRAVDEEEEQTEEDCPELIPIEMREGEEEEKSGPGTKILVTIITRY*GA>GAPILLKNILMEQHKKRVVV

Parental  ILNEFGEGSAVEKSLAVSQGGELYEEWLELRNGCLCCSVK-DNGLRAIENLMQKKGKFDYILLETTGLAD
          I.N.FG..S.VEKSL.VSQ...LY...LELRN.CLC.S...D.G..A.EN.MQKKGKFD.I.L.TTGLAD
Retrocopy ISNKFGGESTVEKSLSVSQSEVLYQK*LELRNDCLCYSTE*DSGPGANENVMQKKGKFDDIPLKTTGLAD

Parental  PGAVASMFW-VDAELGVDIYLDGIITVVDSKYGLKHLEEEKPDGLINEASRQVALADIIIINKTDLVSEE
          .GAVAS.FW.VDAELG..I.L..I.T.VD.KYGLKHL..EK.DGLI.EASRQ.A.AD.IIINKTD.VS.E
Retrocopy AGAVASLFW>VDAELGINISLISIRTLVDTKYGLKHLAVEKLDGLIQEASRQTASADTIIINKTDWVSQE

Parental  DLSKLRAAIRSINGLGKILETQRSRVDLSNVLDLHAFDSLSGISLQK-KLQHVPTTQPHLDQSIITVTF-
          DL.KLR..IRSINGLGK.LETQ.SR.DLSN.L.LH.FDSLSGI.LQK.KLQH.PTTQP..DQSII..TF.
Retrocopy DLNKLRITIRSINGLGKFLETQGSRADLSNILALHVFDSLSGIYLQK<KLQHLPTTQPCADQSIINITF<

Parental  EVPGNAKEESLNVFIQNLLWEKNIRNKDDDCMEVIRLKGLVSIKDKAKQVIVQGVHELYDLEETPLSWKD
          ..P...KEESLN.FIQNLLW.KN.R.KD.DCM.V..LKG.V.IKDK.K..IVQG.HELYDLEE...SWK.
Retrocopy LEPSDVKEESLNGFIQNLLWVKNVRSKDNDCMQVKQLKGQVLIKDKPKPMIVQGAHELYDLEE---SWKE

Parental  DTERTNRLVLIGRNLDKEI-LRQLFVATVTEAEKRWTTHFKEDQV
          DTERTN.L.LI..NLD..I.L..L..AT.TE.EK.WTTHFKEDQV
Retrocopy DTERTNQLALIDGNLDEDI<LQ*LLIATKTETEKWWTTHFKEDQV

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	40.95 RPM
SRP017611_brain	0.00 RPM	21.20 RPM
SRP017611_kidney	0.00 RPM	44.58 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_354 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_354 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001943	1 retrocopy	retro_cfam_354 ,
Sarcophilus harrisii	ENSSHAG00000001103	1 retrocopy	retro_shar_244,
Tupaia belangeri	ENSTBEG00000001371	1 retrocopy	retro_tbel_1641,