RetrogeneDB ID: retro_cfam_291

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:15651764..15652385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSCAFG00000011805
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_cfam_291
GTAACAAATCTTGGTGCTTATATACTTTATTTCATCTTTGCAACACTGAGTTATTATTTTGTCTGTGATCATTTATTAAT
GAAGCATCCATGATTTTTTAAAAATAATGTCTATAGAGAGATTACATTTATTGTCCAATTACTGCCATAATTTAATAGTC
CCACTGTTTCATTGTTTCTCCTAGAGTTGAGAGATTACAGCAAACTATATGATGACCCTGGAGAGTTTCCAGGTGGCTGG
TTTGGGCTCATTGTTAGTATACTCCCCCTCCTCTTTTTCACTAATATGCTGATCTACTGGATTCATAGAGGCCTTCATCA
TAGAACTTGTGTATAAGCACATATACAAACCAAATCATCTCTGGAAGATTCCTACTCCATTTGCAAGTCATGCTTTTCAC
CCTTTGGATGGCTTCCTTCAGAGTCCGCCTTGCCATATAGACTCTTTCATCCTTCCATTACACAGGTAGTTTATTTCAGT
TTGTACATCTTGATCAATATCTGGACAATTTCCATTCATGATGGCAATTTCCATGTTCTCCAAATCTTAAAGACATTTAT
TAATGGCTCAGCCCATCATACAGACCACCACATGTTATTTGACTATAATTATGGACAGCAC

Alignment

ORF - retro_cfam_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 59.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTNLGAYILYFFFATLSYYFVYDHSLMKHPQFLKNQVYREIMFTVQSLPWISIPTVLLFLLELRGYSKLY
          VTNLGAYILYF.FATLSYYFV.DH.LMKHP.F.KN.VYREI.F.VQ.LP....PTV.LFLLELR.YSKLY
Retrocopy VTNLGAYILYFIFATLSYYFVCDHLLMKHP*FFKNNVYREITFIVQLLP*FNSPTVSLFLLELRDYSKLY

Parental  DDIGEFPSGWFRLIISILSFLFFTDMLIYWIHRGLHHR-LVYKRIHKPHHLWKIPTPFASHAFHPVDGFL
          DD.GEFP.GWF.LI.SIL..LFFT.MLIYWIHRGLHHR.LVYK.I.KP.HLWKIPTPFASHAFHP.DGFL
Retrocopy DDPGEFPGGWFGLIVSILPLLFFTNMLIYWIHRGLHHR>LVYKHIYKPNHLWKIPTPFASHAFHPLDGFL

Parental  QSLPYHIYPFIFPLHK-VVYLSLYILVNIWTISIHDGDFRVPQILRPFINGSAHHTDHHMFFDYNYGQY
          QS.P.HI..FI.PLH..VVY.SLYIL.NIWTISIHDG.F.V.QIL..FINGSAHHTDHHM.FDYNYGQ.
Retrocopy QSPPCHIDSFILPLHR<VVYFSLYILINIWTISIHDGNFHVLQILKTFINGSAHHTDHHMLFDYNYGQH

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	27.17 RPM
SRP017611_brain	0.00 RPM	35.89 RPM
SRP017611_kidney	0.00 RPM	26.55 RPM
SRP017611_liver	0.00 RPM	61.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_291 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291 ,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,