RetrogeneDB ID: retro_cfam_1276

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:10224273..10224909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E
• Ensembl ID: ENSCAFG00000010307
• Aliases: None
• Description: eukaryotic translation initiation factor 4E [Source:HGNC Symbol;Acc:3287]

Sequence

>retro_cfam_1276
GAAACCACCCCTACTCCTAATCCCCCGCCTACAGAAGAAGAGAAAACAGAATCTAATCAGGAGGTTGCTAACCCAGAACA
CTATATTAAACATCCTTTACAGAACAGATGGGCACTCTGGTTTTTTAAAAATGATAAAAGCTAAACTTGGCAAGCAAACC
TTCAGCTGATCTCTAAGTTTGATACTGTTGAAGACTTTTGGGCTCTGTACAACCACATCCAGTTGTCTAGTAATTTAATG
CCTGGCTGTGACTACTCACTTTTTAAGGATGGTATTGAGCCTATGTGGGAAGATGAGAAAAACAAATGAGGAGGACGACG
ATGGCTAATTACATTGAACAAACAGCAGAGACGTAGTGACCTGGATCGCTTTTGGCTAGAGACACTGCTGTGCCTTATTG
GAGAATCTTTTGATGACTACAGTGATGATGTATGTGGAGCTGTCGTTGATGTTAGAGCTAAAGGTGATAAGATAGCAATA
TGGACTACTAAATGTGAAAACAGAGAGGCTGTTACACATATAGGGAGAGTATACAAGGAAAGGTTAGGACTTCCTCCAAA
AATAGTGATTGGTTATCAGTCCCATGCAGACACAGCTACAAAGAGTGGCTCCACTGCTAAAAATAGGTTTGTTGTT

Alignment

ORF - retro_cfam_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 97.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETTPTPNPPPTEEEKTESNQEVANPEHYIKHPLQNSWALWFFKNDKSKTWQANLRLISKFDTVEDFWALY
          ETTPTPNPPPTEEEKTESNQEVANPEHYIKHPLQN.WALWFFKNDKS.TWQANL.LISKFDTVEDFWALY
Retrocopy ETTPTPNPPPTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKS*TWQANLQLISKFDTVEDFWALY

Parental  NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGG-RWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY
          NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNK.GG.RWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY
Retrocopy NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNK*GGRRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDY

Parental  SDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRF
          SDDVCGAVV.VRAKGDKIAIWTT.CENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGST.KNRF
Retrocopy SDDVCGAVVDVRAKGDKIAIWTTKCENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGSTAKNRF

Parental  VV
          VV
Retrocopy VV

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	4.58 RPM	32.55 RPM
SRP017611_brain	1.98 RPM	23.34 RPM
SRP017611_kidney	5.75 RPM	51.77 RPM
SRP017611_liver	0.73 RPM	7.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1276 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1276 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009522	3 retrocopies	retro_btau_1094, retro_btau_1702, retro_btau_944,
Canis familiaris	ENSCAFG00000010307	1 retrocopy	retro_cfam_1276 ,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000009450	9 retrocopies	retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Dasypus novemcinctus	ENSDNOG00000013712	5 retrocopies	retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Echinops telfairi	ENSETEG00000007347	3 retrocopies	retro_etel_1285, retro_etel_1449, retro_etel_499,
Macropus eugenii	ENSMEUG00000011104	3 retrocopies	retro_meug_2087, retro_meug_2114, retro_meug_428,
Myotis lucifugus	ENSMLUG00000005035	3 retrocopies	retro_mluc_1519, retro_mluc_24, retro_mluc_474,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Mustela putorius furo	ENSMPUG00000002041	1 retrocopy	retro_mputfur_37,
Otolemur garnettii	ENSOGAG00000001131	1 retrocopy	retro_ogar_259,
Tursiops truncatus	ENSTTRG00000004206	2 retrocopies	retro_ttru_1591, retro_ttru_592,
Vicugna pacos	ENSVPAG00000006072	3 retrocopies	retro_vpac_238, retro_vpac_444, retro_vpac_93,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,