RetrogeneDB ID: retro_vpac_375

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_13745:4085..4938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM66
• Ensembl ID: ENSVPAG00000004766
• Aliases: None
• Description: transmembrane protein 66 [Source:HGNC Symbol;Acc:28789]

Sequence

>retro_vpac_375
GCTCCTACCCTCCACTAGGACCACTACACCACTTCCTGTGGGTTAGATCCAACCCCACACTGAAATGTGTTAGAGGAATA
GCTGGATGACAATCTTATACCCCCAGAGTCATACAGTGTCAGCACGAAGGCTGCAATGGTTATCTGTACAGTGAGGATAT
AAGGCCAATTTAGATATCATTTACCAATTTGGGGAAACTGTGGTGAGCTGTGAAAGATATGAATCCTCTGAAGACTAGTA
TAATATTAAGATGTTCCTCTACCATGGAGTATAACTTCAATTACATCAAACTTGGCCTGAAGAAATTGAGAGTCAGAAAA
AGTCATGGCTTTAGCTCTTTCTCTGATCATGATGGTAAGCTGTACTCCCCAGATTCTTGTGGCATCAGTGGAGTGATCAC
CACGGTGGTGCTACTTGCTGTTGCCTTTGGAGTTTATGAATTGTCCCTTAGTGATGGTCAAGATGCTCTTCCACTATATC
CTGGGTATCCTCCATATTCCCATCATAATCAGAGACTCACCAACTCAACAGGACCCTTCCTGGAGGCTGTAAGTTTGAGT
TCACAGGTCTGCACGGTGCAACTTCTGGCTTTGGCAGTGCTTTCGTAGGACGAGGAAATTAACATTCAGGACCAGGGCTC
TGGACTGGCTTGGGAACATCAGGATATTTGTTTGGCAGCAATAGAGCAGCAACGCCCTTCTCAGACTCATGGTACCACCC
ATCTCACCCTCCCTCACACTCCAGCACACGGAAGAGCCCTGCTTACTGCTTCGGGGAGGCACAGGCAGCTCTTTGGCAGT
CAAGCTCAGAGACAGGATCCAGAACAGCATCAGGATATGGTGGCACCAGAAGG

Alignment

ORF - retro_vpac_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.18 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALTLHHDRYTTSRRLDPIPQ-LKCVGGTAGCDSYTPKVIQCQNKGWDGY-DVQWECKTDLDIAYKFGKTV
          A.TLH.D.YTTS..LDP.P..LKCV.G.AG..SYTP.VIQCQ..G..GY..VQ...K..LDI.Y.FG.TV
Retrocopy APTLH*DHYTTSCGLDPTPH<LKCVRGIAG*QSYTPRVIQCQHEGCNGY<SVQ*GYKANLDIIYQFGETV

Parental  VSCEGYESSEDQY-VLRGSCGLEYNLDYTELGLKKLRESGKNHGFNSFSDYYNKLYSPDSCNISGVLTIV
          VSCE.YESSED.Y..LR.S...EYN..Y..LGLKKLR...K.HGF.SFSD...KLYSPDSC.ISGV.T.V
Retrocopy VSCERYESSED*Y>ILRCSSTMEYNFNYIKLGLKKLRVR-KSHGFSSFSDHDGKLYSPDSCGISGVITTV

Parental  VLLAIAFGVYKFFLSDGQDSPPPYSEYPPYSHQYQRFSNSAGP-PPTGFKPEFTGPHGATYGFGSAFTGQ
          VLLA.AFGVY...LSDGQD..P.Y..YPPYSH..QR..NS.GP..P.G.K.EFTG.HGAT.GFGSAF.G.
Retrocopy VLLAVAFGVYELSLSDGQDALPLYPGYPPYSHHNQRLTNSTGP<LPGGCKFEFTGLHGATSGFGSAFVGR

Parental  GGHENSGPGFWTGLGTGGILGYLFGSNRAATRFSDSWYYPSHPASHSSSWNSRTYSPPGGGPGSYSACSG
          .G...SGPG.WTGLGT.G...YLFGSNRAAT.FSDSWY.PSHP.SHSS...S..Y.............S.
Retrocopy -GN*HSGPGLWTGLGTSG---YLFGSNRAATPFSDSWYHPSHPPSHSSTRKSPAYCFGEAQAALWQSSSE

Parental  SEPRTRTASGYGGTRR
          ...RT..ASGYGGTRR
Retrocopy TGSRT--ASGYGGTRR

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_375 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_375 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012289	1 retrocopy	retro_cjac_399,
Vicugna pacos	ENSVPAG00000004766	1 retrocopy	retro_vpac_375 ,