RetrogeneDB ID: retro_vpac_444

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_198255:358..987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E
• Ensembl ID: ENSVPAG00000006072
• Aliases: None
• Description: eukaryotic translation initiation factor 4E [Source:HGNC Symbol;Acc:3287]

Sequence

>retro_vpac_444
GAAACCACCCCTACTCCTAGTTCTCCGCCTACAGAAGAAGAGAAAACAGCTAATCAGGAGGTTGCTAACCCAAAACACTA
TATTAAACATCCTTTACAGAACAGATGGGCACTCTGGTTTTTCAAAAATGATAAAAGCAAAACTTGGCAAGCAAACCTTC
AGCTGATCTCTAAGGTCGATACTGTTGAAGACTTTTGGGCTCTGTACAACCATATCCAGTTGTCTAGTAATTTAATGCCT
GGCTGTGACTACTCACTTTTTAAGGATGGTATTGAGCCCATGTGGGAAGATGAGAAAAATCACCGAGGAGGACAATGGCT
AATTACATTGAACAAACGGCAGAGACGAAGTTACTTGGATCGCTTTTGGCTAGAGACACTGCTGTGCCTTATTGGAGAAT
CTTTTGATGACTACAGTGATGATGTATGTGGAGCTGTTGCTAGTGTTAGAGCTAAAGGTGATAAGATAGCAATATGGACT
ACTGACTGTGAAAACGGAGACGCTATTACATATATAGGGAGGGTATACAAGAAAAGGTTAGGACTCCTCCAAAGATAGTG
ATTGGTTATCAGTCCCATGCAGACAGAGCTACTAAGAGGGGCTCTACCACTAAAAATAGGTTTGTTGTA

Alignment

ORF - retro_vpac_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETTPTPNPPPTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALY
          ETTPTP..PPTEEEKT..NQEVANP.HYIKHPLQNRWALWFFKNDKSKTWQANL.LISK.DTVEDFWALY
Retrocopy ETTPTPSSPPTEEEKT-ANQEVANPKHYIKHPLQNRWALWFFKNDKSKTWQANLQLISKVDTVEDFWALY

Parental  NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYS
          NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKN.RGG.WLITLNK.QRRS.LDRFWLETLLCLIGESFDDYS
Retrocopy NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNHRGGQWLITLNKRQRRSYLDRFWLETLLCLIGESFDDYS

Parental  DDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGL-PPKIVIGYQSHADTGNKSGSTTKNRF
          DDVCGAV..VRAKGDKIAIWTT.CEN..A.T.IGRVYK.RLGL.PPKIVIGYQSHAD...K.GSTTKNRF
Retrocopy DDVCGAVASVRAKGDKIAIWTTDCENGDAITYIGRVYKKRLGL<PPKIVIGYQSHADRATKRGSTTKNRF

Parental  VV
          VV
Retrocopy VV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_444 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_444 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 36 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,
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,