RetrogeneDB ID: retro_cfam_824

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:38886674..38887560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF346
• Ensembl ID: ENSCAFG00000016541
• Aliases: None
• Description: None

Sequence

>retro_cfam_824
GAGTATCCTGCGCTGAGCACAATGGAGGCCACAGACAGTGGAAGAGCCAGGCCACACAGCAGCTCTCAGGAGCAAGAAGG
ACAAGAACCTCACGGGCTGTGCTTTGACCTCGAGGAGCCCCTCACCTCTAGGAAGCAGTGTCTGGGGGCCCAACCAATGG
GGAGAGAAGAAGTGGAACTCATGATCCAGAAGAACTAGTATCTCTTTACCAGTACCCAGTGTAAGGTTTGCTGCGCCTTG
CTCATTTCCGAATCCCAGGAACTGGCACGCTACCAGAGCAAAAAACATGTCAACAAAGTGAAGAGATGCCTACCAATCCA
TGGAATGGCGACATTAAAAGGGGAAACGAAGAAGCTAGACTCAGGTCAGAACAGCAGAAGCAAAGACAAGAACCAGTGCT
GCCCCTTCTGTAACATGACCTGTTCCTCCCCTGTGGTGGCCCCATCGCAACTATCTAAGACCCACACAAAGAACTTAGAG
CTGCAGCAGCAATCCACTAAGGTGAAAGCTCTGTCAAAATGCTTTGCAAACCCTTTCCTTATGGCCTCCACCTTAGCCTT
GTACCAGGATAGAGAGATGATAGGCCCAGTCAAGTTCTGCAGCCTCGGCCATGCAACTTACAATGACCCTGTCATGGCTC
AATAACATTATGTGGGCAAGAAACACAGGAAACAGGAAACCAGCTCAAATTCACGGCACATTATGGGCAGCTGGCAGACC
CTGCTATTGCTGACGCATCAGCTGAGAAGGCCCACCCCTGCAAGATGTTAAGATAATGCTCAACTCCATAGAACGGTATC
AAGCTCATGTCAGTGGCTGCAAACACAAGAACCAGTCACCAAAAGCAATGGCATCACACCTGAGCCAGATTCCAATGCAA
AGGCAG

Alignment

ORF - retro_cfam_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYRGLGTVEAADSGGARPYNSSEEREGREPDGLRFDRER-ARRLWEAVSG-AQPVGREEVEHMIQKNQCL
          EY..L.T.EA.DSG.ARP..SS.E.EG.EP.GL.FD.E..A..L.EAVSG.AQP.GREEVE.MIQKN..L
Retrocopy EYPALSTMEATDSGRARPHSSSQEQEGQEPHGLCFDLEE<APHL*EAVSG>AQPMGREEVELMIQKN*YL

Parental  FTNTQCKVCCALLISESQKLAHYQSKKHANKVKRYLAIHGMETLKGETKKLDSEQKSSRSKDKNQCCPIC
          FT.TQCKVCCALLISESQ.LA.YQSKKH.NKVKR.L.IHGM.TLKGETKKLDS.Q..SRSKDKNQCCP.C
Retrocopy FTSTQCKVCCALLISESQELARYQSKKHVNKVKRCLPIHGMATLKGETKKLDSGQ-NSRSKDKNQCCPFC

Parental  NMTFSSPVVAQSHYLGKTHAKNLKLKQQSTKVEALSKRLTNPFLVASTLALHQNREMIDPDKFCSLCHAT
          NMT.SSPVVA.S..L.KTH.KNL.L.QQSTKV.ALSK...NPFL.ASTLAL.Q.REMI.P.KFCSL.HAT
Retrocopy NMTCSSPVVAPSQ-LSKTHTKNLELQQQSTKVKALSKCFANPFLMASTLALYQDREMIGPVKFCSLGHAT

Parental  FNDPVMAQQHYVGKKHRKQET-KLKLMAHYGRLADPAVTDSSAGKGYPCK-TCKIMLNSIEQYQAHVSGF
          .NDPVMAQ.HYVGKKHRKQET..LK..AHYG.LADPA..D.SA.K..PCK...KIMLNSIE.YQAHVSG.
Retrocopy YNDPVMAQ*HYVGKKHRKQET<QLKFTAHYGQLADPAIADASAEKAHPCK<DVKIMLNSIERYQAHVSGC

Parental  KHKNQSPKTVASPLGQIPMQRQ
          KHKNQSPK..AS.L.QIPMQRQ
Retrocopy KHKNQSPKAMASHLSQIPMQRQ

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	32.63 RPM
SRP017611_brain	0.00 RPM	27.15 RPM
SRP017611_kidney	0.00 RPM	11.23 RPM
SRP017611_liver	0.00 RPM	3.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_824 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016541	2 retrocopies	retro_cfam_1921, retro_cfam_824 ,
Felis catus	ENSFCAG00000027865	1 retrocopy	retro_fcat_869,
Mustela putorius furo	ENSMPUG00000012295	1 retrocopy	retro_mputfur_271,