RetrogeneDB ID: retro_vpac_458

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_213495:38..470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR1L
• Ensembl ID: ENSVPAG00000004314
• Aliases: None
• Description: mitochondrial fission regulator 1-like [Source:HGNC Symbol;Acc:28836]

Sequence

>retro_vpac_458
CGCAGCTACGTTGAGAAAATAGTGGCAGCCGTGCAGTTCCGGATTCACTAACGCCAGATTTCTTATTTCCAGGAAGTTCA
AATGCCTCTTTTTCCTTACCTTTTTTTTGGATCCTCATTCTGCTCTAAGACATCTCTCGTCATTAGTGACATCACCCAGG
AGACCCAGGAAGAGGTTCCTCCCTCTGCTTTGTTCTGCCAGCCCTGATGTTGCAAACCAGAACACAGAGCTACGTGCTGC
TAGCATCTGAATAGGATGTCTTCATCTCTGTCCCAGGCCAGCAGCTTTGTAGATATGATGGGTATCCTAAAGGACTTTCA
CCAGAAGCAGCAGAGCCAAGATCCGAACCGGAGTTTATAGAAGGAGGAAGACCCTGCTGGCCAAATCTCTAAGGTCCTAA
AGAGGAAGTTCGCTCTGAAGAAAGAAGTTATC

Alignment

ORF - retro_vpac_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSQIAKIVAG-DAASASLTPDFLSPGSSNVSS-PLPCFGSSFHSTTSFVISDITEETEVEVPELPSVPLL
          RS...KIVA...A...SLTPDFL.PGSSN.S..P....GSSF.S.TS.VISDIT.ET..EVP..PS..L.
Retrocopy RSYVEKIVAA<RAVPDSLTPDFLFPGSSNASF>PYXXXGSSFCSKTSLVISDITQETQEEVP--PSA-LF

Parental  CSASPECCKPEHKATCSSSEEDDCVSLSKASSFADMMGILKDFHRMKQSQDLNRSLLKEEDPGVLIFYVL
          C...P.CCKPEH.ATC.........SLS.ASSF.DMMGILKDFH...QSQD.NRSL.KEEDP...I..VL
Retrocopy C--QP*CCKPEHRATCC*HLNRMSSSLSQASSFVDMMGILKDFHQKQQSQDPNRSL*KEEDPAGQISKVL

Parental  RRKGARAEEYI
          .RK.A...E.I
Retrocopy KRKFALKKEVI

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_458 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_458 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000012794	1 retrocopy	retro_fcat_667,
Macropus eugenii	ENSMEUG00000016175	4 retrocopies	retro_meug_1948, retro_meug_2133, retro_meug_359, retro_meug_557,
Myotis lucifugus	ENSMLUG00000010738	1 retrocopy	retro_mluc_338,
Tursiops truncatus	ENSTTRG00000012479	2 retrocopies	retro_ttru_1262, retro_ttru_327,
Vicugna pacos	ENSVPAG00000004314	1 retrocopy	retro_vpac_458 ,