RetrogeneDB ID: retro_cfam_800

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:24027990..24029541(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030026
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCYL2
• Ensembl ID: ENSCAFG00000006752
• Aliases: None
• Description: SCY1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:19286]

Sequence

>retro_cfam_800
CATCCTTTAGAAGAATCCAGAGATTGCTTGGCATTTTGTACCGAACCCATTTTTGCCAGTTTAGCCAATGTTTTAGGTAA
CTGGGAAAATCTACCTTCTTCTGTATCTCTAGACATTAAGGATTATAACCTTTATGATGTCGAAACTAAATATGGTTTGC
TTCAGGTTTCTGAAGGACTGTCATTTTTGCATAGCAGTGTGAAAATGGTCCATGGAAATATTACACCTGAAAATATAATT
TTGAATAAAAGTGAGCCTGGAAATAAGGTGCTTTGATATTTGTGTATCATCAACCAATCCTTGTGAACAAGAGCCTAAGT
TACCTTGTAAAGAATGGGACCCAAATTTACCATCATGTGTCTTCCAAATCGTGAATATTTGGGTCCTGAATACATGCTTC
CGGTGAGCTGTGAAATAGCTAGTGATATGTACTCACTAGGAACTGTCAAGTATGCTGTATTTAATAAAGGAAAACCCATA
TTTGAAGTTAACAAGCACGACATTTACAAGAGTTTTAGTAGACAGTTGGATCAGTTGAGTCGTTTAGGATCTAGCTCACC
TTCAAATATACCCGAGGAAGTCCAAGAACACATAAAACTGCTCTTAAATTAACTCCAACTGTAAGATGAGAAGCAGATCA
AATGACAAAGAATTTCTTCTTCAGTGATGTTGGTGCAATAACACTGCAGTATTCTGAGACCTCATTCCAAAGAGATAATC
TTCAGAAATCACAGTTTCTCAAAGGACTGCCAAAAGTTCTACCAAAACTGCCCAAGCGTGTGCAGGGAATTTGTGCCTTG
TTTGACTTCAGAACTTGTAACCCCTGACATGGTATCTTTTGTTTTGCCCACTGTTCTACTGATTGCCAAAGAAGGCTCCA
AGGAAGCACATGTCAAATTAAGTCTACCTGAACGTGGCTCTGTCTTTAAACAGCAGGAGCCCATCCAGGTTGTTAATTTA
CTTACAAAAAAAAATGGATTTGCTGCTAACCAAAACTCCTCCTGAGGAGATAAAGAGCAATGTCCTACCAATGGTTCACA
CAGCACTAGAGGCTCCTTCCATTCAAATTCAGGAACTCTGTTTAAACATCATTCCAAGCTTTGCAAGTCTTATAGACTAT
GCATTCATGAAAAATTCTTTGATACCAAGAATTAAAAATGCATGTCTGCAAACGTCTTCTCTTGCTGTTCACGTCAATTC
ATTAGCGTGCTTAGGAAAGATTTTGGAATACTTGGATAAGTGGTTTGTACTTGATGACATCCTGCCCTTCTTACCATAAA
TTCCATCCAAGGAACCCACAGTCCTCATGGGAATTTTAGGTACTTACAAATGTACGTTTACTCATAAGAAGTTGGGAATC
ACCAAAGAACAGTGGCTGGAAAAGTATTGGCTCATCTGATTCCCCTGAGTATTGAAAATAATCTTAATCTCAATCAGTTC
AATTCTTTCATTTCTGTCATAAAAGAGACGCTTAACAGATTGGAAACTGAACATAAGACTAAACTGGAGCAACTTCATAT
AATGCAAGAGCAGCAGAAAAGGTTACAAATG

Alignment

ORF - retro_cfam_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  HPLEESRDCLAFCTEPVFASLANVLGNWENLPSPVSPDIKEYNLYDVETKYGLLQVSEGLSFLHSSVKMV
          HPLEESRDCLAFCTEP.FASLANVLGNWENLPS.VS.DIK.YNLYDVETKYGLLQVSEGLSFLHSSVKMV
Retrocopy HPLEESRDCLAFCTEPIFASLANVLGNWENLPSSVSLDIKDYNLYDVETKYGLLQVSEGLSFLHSSVKMV

Parental  HGNITPENIILNKSG-AWK-IMGFDFCVSSTNPSEQEPKFPCKEWDPNLPS-LCLPNPEYLAPEYILSVS
          HGNITPENIILNKS..AWK.I..FD.CVSSTNP.EQEPK.PCKEWDPNLPS..CLPN.EYL.PEY.L.VS
Retrocopy HGNITPENIILNKSE<AWK<IRCFDICVSSTNPCEQEPKLPCKEWDPNLPS<MCLPNREYLGPEYMLPVS

Parental  CETASDMYSLGTVMYAVFNKGKPIFEVNKQDIYKSFSRQLDQLSRLGSSSLSNIPEEVREHVKLLLN-VT
          CE.ASDMYSLGTV.YAVFNKGKPIFEVNK.DIYKSFSRQLDQLSRLGSSS.SNIPEEV.EH.KLLLN..T
Retrocopy CEIASDMYSLGTVKYAVFNKGKPIFEVNKHDIYKSFSRQLDQLSRLGSSSPSNIPEEVQEHIKLLLN<LT

Parental  PTVRPDADQMTKIPFFDDVGAVTLQYFDTLFQRDNLQKSQFF-KGLPKVLPKMPKRVIVQRILPCLTSEF
          PTVR..ADQMTK..FF.DVGA.TLQY..T.FQRDNLQKSQF..K...K.....P.........PCLTSE.
Retrocopy PTVR*EADQMTKNFFFSDVGAITLQYSETSFQRDNLQKSQFL>KDCQKFYQNCPS--VCREFVPCLTSEL

Parental  VNPDMVPFVLPNVLLIAEECTKEEYVKLILPELGPVFKQQEPIQI-LLIFLQKMDLLLTKTPPDEIKNSV
          V.PDMV.FVLP.VLLIA.E..KE..VKL.LPE.G.VFKQQEPIQ..L.......DLLLTKTPP.EIK..V
Retrocopy VTPDMVSFVLPTVLLIAKEGSKEAHVKLSLPERGSVFKQQEPIQV>LIYLXXXXDLLLTKTPPEEIKSNV

Parental  LPMVYRALEAPSIQIQELCLNIIPTFANLIDYPSMKNALIPRIKNACLQTSSLAVRVNSLVCLGKILEYL
          LPMV..ALEAPSIQIQELCLNIIP.FA.LIDY..MKN.LIPRIKNACLQTSSLAV.VNSL.CLGKILEYL
Retrocopy LPMVHTALEAPSIQIQELCLNIIPSFASLIDYAFMKNSLIPRIKNACLQTSSLAVHVNSLACLGKILEYL

Parental  DKWFVLDDILPFLQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQ-LAGKVLPHLIPLSIENNLNLNQF
          DKWFVLDDILPFL..IPSKEP.VLMGILG.YKCTFTHKKLGITKEQ..AGKVL.HLIPLSIENNLNLNQF
Retrocopy DKWFVLDDILPFLP*IPSKEPTVLMGILGTYKCTFTHKKLGITKEQ<VAGKVLAHLIPLSIENNLNLNQF

Parental  NSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDI
          NSFISVIKE.LNRLE.EHKTKLEQLHIMQEQQK.L..
Retrocopy NSFISVIKETLNRLETEHKTKLEQLHIMQEQQKRLQM

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	52.58 RPM
SRP017611_brain	0.00 RPM	57.56 RPM
SRP017611_kidney	0.00 RPM	52.17 RPM
SRP017611_liver	0.00 RPM	28.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_800 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_800 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006752	1 retrocopy	retro_cfam_800 ,
Sarcophilus harrisii	ENSSHAG00000011140	1 retrocopy	retro_shar_569,