RetrogeneDB ID: retro_cfam_1339

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:30731598..30732334(+)
• Located in intron of: ENSCAFG00000009352

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSCAFG00000006884
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_cfam_1339
TTGCCTATCCCTTCCCCCTGCAGCTGTGTGGTCTGGCTGCACTTGGGCCATTTTGGCCTCCCATCATGGACAGCCACCAT
GCAACGAGGGTGCTGCCCGTTATTAGGACCCTGCTGAGAACCGCTGACAAGCATTCAGTGGAAATCACTAACAGCTGCTT
TTCAGTGCCTCACAAGGAGTCAAAAGATGAGGTATCTGTTGACATTAAATTCGCTGAGAGTATGTATGAATTAAACAAAG
TCTCTCCAGAAGAGCTCATCCTGTGCTGGTACCCGACAGGCCATGACATTATAGAGTACCCTGTGCTGATCCAGGGGTAC
TACGGCAGGAAAGTCCCTGTCCCTATTCACCTCACTGTGGACAGGAGCCTCCAGAACGGCCACATGAGCACCAAAGCCTA
CGTCAGCACTTTAATTGGTGTCCCTGGGAGTACCATGGGGGTGATGTTCACACCTTGACAGTGGAATATGCATATTATGA
CACTGAACACATTGGAGTTGACCTGATCCTGAAGACCTGTTTTAGCCCCAACCAAGTGTACAGACTGTCAGTCAATTTGC
AGCAGGTAGGACGGGCATCAGTTCACATCTAGGATGTCCTAAGCACAGCGTTGCAGTATACAGATGATGTGCTGTTGGGA
AAGGCATCCACTGACAATATCTCCTGCTGCTTGATGAGTCTGGTTAACCAAGTACACAAGATAATCCCCAGTGATGTTGA
GACCATGCTCAATAGC

Alignment

ORF - retro_cfam_1339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.25 %
• Parental protein coverage: 76.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LPGPFPGGRVVRLHP-VILAS-IVDSYERRNEGAARVIGTLLGTVDKHSVEVTN-CFSVPHNESEDEVAV
          LP.P.P...VV.LH...ILAS.I.DS..........VI.TLL.T.DKHSVE.TN.CFSVPH.ES.DEV.V
Retrocopy LPIPSPCSCVVWLHL>AILAS>IMDSHHATR--VLPVIRTLLRTADKHSVEITNSCFSVPHKESKDEVSV

Parental  DMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSRKAPNPIHLTVDTSLQNGRMSIKAYVS
          D..FA..MYEL.K.VSP.ELIL.WY.TGHDI.E..VLI..YY.RK.P.PIHLTVD.SLQNG.MS.KAYVS
Retrocopy DIKFAESMYELNK-VSPEELILCWYPTGHDIIEYPVLIQGYYGRKVPVPIHLTVDRSLQNGHMSTKAYVS

Parental  TLMGVPGRTMGVMFTP-LTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVL
          TL.GVPG.TMGVMFTP.LTV.YAYYDTE.IGVDLI.KTCFSPN.V..LS..LQQVG.AS..I.D.LST.L
Retrocopy TLIGVPGSTMGVMFTP<LTVEYAYYDTEHIGVDLILKTCFSPNQVYRLSVNLQQVGRASVHI*DVLSTAL

Parental  QYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNS
          QY..DVL.GK.S.DN.....LMSLVNQV.KI.P.D.ETMLNS
Retrocopy QYTDDVLLGKASTDN-ISCCLMSLVNQVHKIIPSDVETMLNS

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	0.21 RPM	80.55 RPM
SRP017611_brain	0.48 RPM	43.43 RPM
SRP017611_kidney	0.07 RPM	92.39 RPM
SRP017611_liver	0.07 RPM	64.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1339 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1339 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339 ,
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,