RetrogeneDB ID: retro_cfam_2148

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:39995026..39996283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF1
• Ensembl ID: ENSCAFG00000014239
• Aliases: None
• Description: splicing factor 1 [Source:HGNC Symbol;Acc:12950]

Sequence

>retro_cfam_2148
CCTGACCCTGAGCCCATCTACAATAGGGAGGCAAAGAGGCTTAACACCTGGGAGTTCTGCACCAGCAAAACGCTTGAAGA
AGAGCAGCACAATCTCACCGGAGATGGTTGCCCTCAACCCTGATTTTGAGCCTCCTGCAGATGACAAACTTCCAGCAACA
TGTGTGAGCCATAAAGTAGTGAGTCCACAAGATGAGTATCCAGAAATCAACTTCTTGGGGCTGCTGATTGGGCCCAGTGG
GAACATCTTGAGGAACATAAAGAAGGAATGTAATGTCAAGATTGTGATCGGGGGAAATGGGTCTGTCAAGGAAAAGCAGG
GAGCAAAGATGGCCAGATGTTGCCCAGAGAAGGTGAGCCACGTCATGCCCTAGCTTCTGCCAACACCATGGAAAATGTGA
AGAAAGCCCTGGAACAGATAAGAAGCATCCAGAAACAGGCTATTGAGACCCCTGCAGATCAGGATGATCTATGGAAGATG
CAGCTTCGGTAGTTGGCTTGCCTGAATAGGACTCTTCAGGAATATGATAACAGGATCTTAAGACCCTGGCAGAGCTCAGA
GACTCACAACATTGCCAATACCACAGTGCACACCAAGTGTGGTCACAAAGCTTTTGATTGCAAATTCCAAAGGCCTGATG
ACACCCAGTCAGCTCAAGATAAAGCATGGATGGATAAAGAATCTTTGTCCCTTAGGGCTGAACTTGGTGAAGCACCTATG
GACTCTACCTCTGGGCCCACCACCACGCCCCTGGACAGTGCACCTTGGCCTGCTGCTCCCACCAACAATCCACCTCCACC
ATCTCTCATGGCCACTACCCAGAGCTGCCCACTCTAGATGATGAATTTTGGCACTTCAGAGAGTTGGCCCTACCATGGCA
TGCACAGAGGTGGTCTTGGTGGGCCTGGAGGTGGCCCCCACAGCCTCCCACACCCATTACCCAGCCTGACAGGTAGGCAT
GCTGGACATCCCATGCAGCATAACCTTAATGGACCCCCACTTCCTTGAATGCAGCCACTACCACCACAGATGGACCAGGG
CCCCACCCACCTGGGTACCATTGCCCTCTTCCAGTGGATCAGTAACTGGGAAGTATGCCTGTGGGTTCTGGGGTCTCTTG
CTTGCTTCAAGGAAAAGATATGATGCCATCTATGGGTGTGATGCTGGCACCATGCCCTCTTTCTTCCCCCATGGCAGCAG
CAGCCTCCATCACCCTGTCTGCCCAACAGCAGTATGGCTTCCAGGAGCCCCTTGCCA

Alignment

ORF - retro_cfam_2148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PSPEPIYNSEGKRLNTREFRTRKKLEEERHNLIT-EMVALNPDFKPPADYKPPATRVSDKVMIPQDEYPE
          P.PEPIYN.E.KRLNT.EF.T.K.LE.E.....T.EMVALNPDF.PPAD.K.PAT.VS.KV..PQDEYPE
Retrocopy PDPEPIYNREAKRLNTWEFCTSKTLE-EEQHNLT>EMVALNPDFEPPADDKLPATCVSHKVVSPQDEYPE

Parental  INFVGLLIGPRGNTLKNIEKECNAKIMI-RGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKA
          INF.GLLIGP.GN.L.NI.KECN.KI.I.RGK..V..GK.G.KDGQMLP.E.EP.HAL..ANTMENVKKA
Retrocopy INFLGLLIGPSGNILRNIKKECNVKIVI<RGKW-VCQGKAGSKDGQMLPREGEPRHALASANTMENVKKA

Parental  VEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHI
          .EQIR.I.KQ.IETP.DQ.DL.KMQLR.LA.LN.TL.E.DNRILRPWQSSET..I.NTTV.TKCG...H.
Retrocopy LEQIRSIQKQAIETPADQDDLWKMQLR*LACLNRTLQEYDNRILRPWQSSETHNIANTTVHTKCG---HK

Parental  ASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSL
          A.DCKFQRP.D.QSAQDKA.MDKE.LSL.AELGEAP......STSGP.TTPL.SAP.PAAP.NNPPPPSL
Retrocopy AFDCKFQRPDDTQSAQDKAWMDKESLSLRAELGEAP----MDSTSGPTTTPLDSAPWPAAPTNNPPPPSL

Parental  MSTTQSRPP-WMNSGPSESRPYHGMHGGGPGGPGGGPHSFPHPLPSLTGGHGGHPMQHNPNGPPPPWMQP
          M.TTQS.P...MN.G.SES.PYHGMH.GG.GGPGGGPHS.PHPLPSLTG.H.GHPMQHN.NGPP.P.MQP
Retrocopy MATTQSCPL*MMNFGTSESWPYHGMHRGGLGGPGGGPHSLPHPLPSLTGRHAGHPMQHNLNGPPLP*MQP

Parental  PPPPMNQ-GPHPPGHHGPPPMDQYLGSTPVGSGVYRLHQGKGMMPPPPMGMMPPPPPPPSGQ-PPPPPSG
          .PP.M.Q.GPHPPG.H.P.P.DQ.LGS.PVGSGV..L.QGK.MM..P.MG.M..P.P..S......PPS.
Retrocopy LPPQMDQ<GPHPPGYHCPLPVDQ*LGSMPVGSGVSCLLQGKDMM--PSMGVMLAPCPLSSPM>QQQPPSP

Parental  PLPPWQQQQQQPPP
          .LP........P.P
Retrocopy CLPNSSMASRSPLP

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	201.13 RPM
SRP017611_brain	0.00 RPM	102.26 RPM
SRP017611_kidney	0.00 RPM	69.34 RPM
SRP017611_liver	0.00 RPM	86.58 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2148 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017828	1 retrocopy	retro_amel_1763,
Canis familiaris	ENSCAFG00000014239	1 retrocopy	retro_cfam_2148 ,
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930,
Ictidomys tridecemlineatus	ENSSTOG00000009790	1 retrocopy	retro_itri_698,