RetrogeneDB ID: retro_vpac_326

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_878:1900649..1901159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCML1
• Ensembl ID: ENSVPAG00000003425
• Aliases: None
• Description: sex comb on midleg-like 1 (Drosophila) [Source:HGNC Symbol;Acc:10580]

Sequence

>retro_vpac_326
AAGATGTCAAGCGGCTCCAGTGAAATTAATGTGATAAGAACACAAATCTCTGCTTATGATGATGATAACACTGTTCTTTA
CGCATACGAACCAAATACGGCATTTTTCAATAATCAGGAAAATATTGTGTCTGACACAGCCTACAACGAAGAGCACCAAA
AAACAGTTCTGGATGTCCTTACTCACTGCCAGGTCATCTATGATGCTATTCAAAACCTGGATAAGAAGTTCGATGTTCTT
CATGGAAAGGTTACAAAAATCCACCGTCTTCGTATGAAGTCATTGTGGCAAACTCGTAAGCCACTTGGATATGCATATAA
AAATTATAATTACCTGCTTTCTAAAAAGGTCAAATCCCAGAAACTGCGCAAAAAGGAACCTCGCGCTACATTCTCCTACC
CTGAAAGTTACAGCCCAACTACACCAGTAGGAAGGCGGGACATTGATTCCTATAGCAACCTCGGAGGCGGGTCTTTTCAC
TCCGACGAGTCCCTGGATCAGGAGCCAGAG

Alignment

ORF - retro_vpac_326 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 53.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMSSGSSEIDVIRTRISTYDDDNTVLYAYEPNTAFFNN-ENIVSDTAYNEEQQKTVLDVLTHCQVIYDAI
          KMSSGSSEI.VIRT.IS.YDDDNTVLYAYEPNTAFFNN.ENIVSDTAYNEE.QKTVLDVLTHCQVIYDAI
Retrocopy KMSSGSSEINVIRTQISAYDDDNTVLYAYEPNTAFFNNQENIVSDTAYNEEHQKTVLDVLTHCQVIYDAI

Parental  QDLDKKFDVIHGKVTKIHRFRMKSLWQTRKPLGYAYKNYNYLLSKKVKSQGLRKKEP-AAFSYPESYSPT
          Q.LDKKFDV.HGKVTKIHR.RMKSLWQTRKPLGYAYKNYNYLLSKKVKSQ.LRKKEP.A.FSYPESYSPT
Retrocopy QNLDKKFDVLHGKVTKIHRLRMKSLWQTRKPLGYAYKNYNYLLSKKVKSQKLRKKEPRATFSYPESYSPT

Parental  IPVGRRDIDSYSNFGGRSFHSDESLRADQEQE
          .PVGRRDIDSYSN.GG.SFHSDESL..DQE.E
Retrocopy TPVGRRDIDSYSNLGGGSFHSDESL--DQEPE

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_326 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_326 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004677	1 retrocopy	retro_cjac_239,
Vicugna pacos	ENSVPAG00000003425	1 retrocopy	retro_vpac_326 ,