RetrogeneDB ID: retro_cfam_131

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:25814515..25816336(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016289
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000002736
• Aliases: None
• Description: None

Sequence

>retro_cfam_131
ATGCTGCATCAAGCACTTCACAGATTTGGTAAAAACCTGAGACATAGACATCCGCTGGAGCAACCTGTGGCTGAACCTGC
CCCTGCCAGGAGCCTGAGCACTCTGGATTTAGTAGGCCTGGGTGTGGGCCGCACAGTGGGTGTAGGTGTGTATATCTTGG
CTGGTGAGGTGGCTAGAGATAAAGCAGGACCATCCATTGTGATCTGCTTGCTGGTGGCCAGCCTATCTTCTATGTTGGCT
ATGCTGTACTTTGCAGAGTTTAGTCCCCAGATTATCCACTCTGGCTCCAAACATCCCCACAGCTTTGTCATCATAGATAA
ACTTGGGGCTTTCATCACTGCCTGGATTCTCATTCTCAACAATGTTACTGCTATAGCCATTAGGATCTGGGCTTGGACCT
TAGCTCTTGACAACCTTTTTGGAAACAAGATATCTCAGACCTTGCAGGAGACAATTTCACGACATGTTCCCAGGGTCTTT
GCAGAAGTTCTAGGCTTCTTTTTTATGTTCCTTGTGTTGTTGCTCATGGGATTGCTGACTCGGAACATTAGGCAGCTTTC
CCTGGTTACCAAAGTGGTCACATTGGTGAACCTCTTGGTTCTTGGTTTTGTCATCATCTATGGCTTCCTGAAAGGGGACC
TGCACAACTGGAAGCTCACAGAAGAAGACTACATAATGGCTGGACTCAATGACACTTCTAGCTTGGGACCTCTGGGCTCT
GGAGGATTTATGCCTTTTGGCTTCCAGGGGATACTCCATGGATCAGCTACCTGTATCTATTCTTTTACAGGCTTGAGCAT
TATTGTTACCAGATTTGAAGTAGCCCAGAATTTCCAGCATTCCTTTCCTATGTTCATTGTGATTTCACTGCTCATCTGCA
TTTTGGTGTACTGTGGTGTCTTTTCAGCACTTATGCTTATGGTGCCTTATTACCAGCTCCAACCTGGGAGCACCTTGCCT
GAGGCATTTCTCCATACTGGCTGGGCCCCTGCCTACTATGTTGTAACTTTTGCATTCTTCTGTAGTATTTCTGTCAGCCT
CTTGGATTATATGTTTCCCATACGTCAGCTAATCTCCATGATGGCACATTATGGCCTCTTTTTTCCTGTCCTTGCAAGGA
TGCAAACCAGCACATACACACCCATTGTAGCCACTGTGATCTTTGGGATTATTGCAGGAATCATGGTATTATTCTTTGGA
TTTGCCAATCTCTTGGACCTCATGTCAGTTGGGGCCCTGCTAGTTTACTCCCTGCTGGCTTTTAGTGTTCTCATCCTCAG
GTATGAGCCTCAGAGGAGGAATGGGGGAAATGAAGCACAGGTGCAGGAGGAAAATGAAGCAGAGATGCAGGAGGAGAATG
AGGAAAATGAGGCAGAGGTGCAGGAGGAGAACAGACCTGCAGCAGAGAAGCTGACTCTACAGGGACTATTTTTTCCAGGC
AGCCCCACCCCCACTCCACTCTCTGGTCGGGTTGTCTATGTTTGCTCCTCACTGCTCGCTCTGCTGCTGACTCTTCTCTG
CCTGGTGCTGGCCCGGTGGCCAGATCTGCTTTCTGGAGACCCAGTGTGGATCACAGTGGTTGTGCTGCTCCTGGTGCTCA
TCACTGGAGTCACTGGAGTCATCTGGAGACAGCCACAGAACTCCACTCCCCTTCACTTCAAGGTACCTGGTCTGCCTCTC
CTCCCACTCCTGAGCATCTTTCTCAATGTTTATCTTATGGTACAGATGACAGCTGGCACCTGGGCCCTATTTGGTGTCTG
GATGCTGATTGGGTTTGCTATCTACCTTGCTTATGTGATCCAGCAGCACCTGGTTCCTTAG

Alignment

ORF - retro_cfam_131 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLCQHVCQFGQKLLRRRPLGPKQGAESHLARCLNTLDLVALGVGSTLGAGVYILAGEVAKDKAGPAIIIC
          ML.Q....FG..L..R.PL.....AE...AR.L.TLDLV.LGVG.T.G.GVYILAGEVA.DKAGP.I.IC
Retrocopy MLHQALHRFGKNLRHRHPL-EQPVAEPAPARSLSTLDLVGLGVGRTVGVGVYILAGEVARDKAGPSIVIC

Parental  FLVAALSSVLSGLCYAEFGARVPGSGSAYLYSYVTVGQLCAFITGWNLILSYVIGAASVARAWSSAFDDL
          .LVA.LSS.L..L..AEF......SGS....S.V....L.AFIT.W.LIL..V...A....AW..A.D.L
Retrocopy LLVASLSSMLAMLYFAEFSPQIIHSGSKHPHSFVIIDKLGAFITAWILILNNVTAIAIRIWAWTLALDNL

Parental  TGNQVSRVLQGSFSLQAPHVLATHLDFFALGLVLLLTGLLVLGASESALVTKIFTGVNVLVLSFIILSGF
          .GN..S..LQ...S...P.V.A..L.FF...LVLLL.GLL........LVTK..T.VN.LVL.F.I..GF
Retrocopy FGNKISQTLQETISRHVPRVFAEVLGFFFMFLVLLLMGLLTRNIRQLSLVTKVVTLVNLLVLGFVIIYGF

Parental  IKGDLHHWQLTEEDYKLAMSASNDTSSLGPLGSGGFMPFGFEGILHGAATCFYAFIGFDCIATTGEEARD
          .KGDLH.W.LTEEDY...M...NDTSSLGPLGSGGFMPFGF.GILHG.ATC.Y.F.G...I.T..E.A..
Retrocopy LKGDLHNWKLTEEDY--IMAGLNDTSSLGPLGSGGFMPFGFQGILHGSATCIYSFTGLSIIVTRFEVAQN

Parental  PQRSIPLSIIISLFICFLAYFGVSAALTLMMPYYQIHPGSPLPQAFLYVGWAPARYTVAAGTLCALSSSL
          .Q.S.P..I.ISL.IC.L.Y.GV..AL.LM.PYYQ..PGS.LP.AFL..GWAPA.Y.V.....C..S.SL
Retrocopy FQHSFPMFIVISLLICILVYCGVFSALMLMVPYYQLQPGSTLPEAFLHTGWAPAYYVVTFAFFCSISVSL

Parental  LGTMFPMPRVIYAMADDGLLFRGLARIHPCTHTPMMATIVSGTFAAFMAFLF---ELSDLVDL--MSIGT
          L..MFP....I..MA..GL.F..LAR....T.TP..AT...G..A..M...F....L.DL..........
Retrocopy LDYMFPIRQLISMMAHYGLFFPVLARMQTSTYTPIVATVIFGIIAGIMVLFFGFANLLDLMSVGALLVYS

Parental  LLAYSLVVFSVLVLRYQPDQNLSKNEKTEMEIIERKPAPQASSLKSVPEAGTVQALWSLCNPVNTTPTLK
          LLA.S.........R..........E..E.E..E......A........A.....L..L..P...TPT..
Retrocopy LLAFSVLILRYEPQRRNGGNEAQVQEENEAEMQEENEENEAEVQEENRPAAEKLTLQGLFFPGSPTPTPL

Parental  SGHIAYGCALLLALLLTILCLILAQWPSHLFSGDPVYITGCVLLLLLIIGLTFIIWRQPQNPTPFHFKVP
          SG...Y.C..LLALLLT.LCL.LA.WP..L.SGDPV.IT..VLLL.LI.G.T..IWRQPQN.TP.HFKVP
Retrocopy SGRVVYVCSSLLALLLTLLCLVLARWPD-LLSGDPVWITVVVLLLVLITGVTGVIWRQPQNSTPLHFKVP

Parental  ALPVLPLVSIFTNVYLMMQMTSGTWARFGVWMVIGFAIYFGYGIRHSL
          .LP.LPL.SIF.NVYLM.QMT.GTWA.FGVWM.IGFAIY..Y.I...L
Retrocopy GLPLLPLLSIFLNVYLMVQMTAGTWALFGVWMLIGFAIYLAYVIQQHL

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	0.17 RPM
SRP017611_brain	0.00 RPM	0.24 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_131 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_131 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002736	2 retrocopies	retro_cfam_131 , retro_cfam_221,
Canis familiaris	ENSCAFG00000016908	2 retrocopies	retro_cfam_130, retro_cfam_156,