RetrogeneDB ID: retro_vpac_170

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2331:456795..458188(+)
• Located in intron of: ENSVPAG00000007866

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP18
• Ensembl ID: ENSVPAG00000010164
• Aliases: None
• Description: UTP18 small subunit (SSU) processome component homolog (yeast) [Source:HGNC Symbol;Acc:24274]

Sequence

>retro_vpac_170
GAGGGGCTGGTCTTCAGCGACGCCGAGGAAGAGGAGGGCGTGCTGCTGCGGCATCTACGGGGCCCACGGGGTCAAGTACA
GAAGGCTTAGGTGACTCAAGTGGAGAATGAAGCAAAAGATAATTCTCCACCTCGAAAGAAGCCGGCTTGGCTGGATGGAG
AAGATGAAGATGAGGAGATGGTTGACATGATGAACAATCGTTTTCGGAAAGATAGGATGAAAACGCTGCTGAAAGTAAAC
TTTCAGAAGACGAGCTACAAAAGAGGCTGAAAGAAGAATTCCAGCATGCCATGGGGGGAGTACCTGCCTGGGCAGAGACC
AACAGATGGAAAATATTTCCAGATGATGAAGGTGAAGAGGATGAAGATGATTTGTTGCAAAGGCTGGGAATTTCCTGTCC
ACATCAGTCACTCTTCCTAAAGGAATCTTGAAGACTGAAGAACTGCCAACATGCTAATGCTGAACGTCCCACCACTGTTC
GGATCTCGTCTGTGCCGTTCCATCCCTGTGCACAGGCTGTGATGGTCACTGGACTGGATAACACTGTATGGCTCTTTCAG
GTTGATGGAAAAACAAATCCTAGAATTCAGAGTATCTATTTGGAAAAGCTTCCAATCTTTAAGGCTTGTTTCAGTGCTAA
TGGAGAAAAGGTTTTAGCCACGAGCACTCACAGCGAAGTTTTTTTACGTCTATGATATGCTGGCTGAGAAGCTAATTCCT
GTGCGTCAAGTAAGAGGTTTGAAGGAGAAGATAGTGCGGAGCTTCGAAGTCTCCCCAGATGCATCCTTCTTGCTTATTAA
TGGTGTTGCTGGATATTTTCATTTGTTGTCAATGAAGACTAAAGAACTAATTGGTAGCATGAAAATTAATGGAAGGACTG
CAGCATCTACATTCTCTTCAGACAGTAAGAAAGTCTATGCCTCTTCAGGGGATGGAGAAGTTTATGTTTGGGATGTGAAC
TCTAGGAAGTGCCTTAACAGATTTGTTGATGAAGACAGTTTATATGGATTAAGCGTTGCCACATCTAGGAATGGACAGTA
TGTGGCTTGTGGTTCCAATTGTGGAGTGGTAAACATATACAGTCAAGATTCTTGTCTCTAAGAAACAAACCCAAAGCCAA
TAAAAGCTACAATGAACTTGGTTACAGGTGTTACTTCTCTGACCTTCAATCCTACTACAGAAATCTTGGCAATTGCTTCA
GAAAAAATGAAAGAAGCAGTCAGATTGGTCCACCTTCCTTCCTGTATAGGATTTTCAAGCTTCCCAGTTGTTAAAAAGAA
GAATATTTCTCTTGTTCTATGCTACGGATTTTTCTTCCAGAAGTGGATATTTTGCCTTGGGGAATGAAAAGGGCAAAGCC
CTGATGAATAAGTTGCATCATTACTCAGACTTT

Alignment

ORF - retro_vpac_170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.47 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EELVFGDVEEDEDALLRRLQGPRVQVREDSGDSEVENEAKDDFPPQKKPVWLDEEDEDEEMIDMMNNRFR
          E.LVF.D.EE.E..LLR.L.GPR.QV........VENEAKD..PP.KKP.WLD.EDEDEEM.DMMNNRFR
Retrocopy EGLVFSDAEEEEGVLLRHLRGPRGQVQK-A*VTQVENEAKDNSPPRKKPAWLDGEDEDEEMVDMMNNRFR

Parental  KGMMK-NATESKLSKDELQKRLKEEFQHAMGGVPAWAETNRRKTSSDDESEEDEDDLLQR-TGNFLSTSA
          K..MK.NA.ESKLS.DELQKRLKEEFQHAMGGVPAWAETNR.K...DDE.EEDEDDLLQR..GNFLSTS.
Retrocopy KDRMK<NAAESKLSEDELQKRLKEEFQHAMGGVPAWAETNRWKIFPDDEGEEDEDDLLQR<AGNFLSTSV

Parental  TLPKGILK-MKNCQHANAERPTTARVSSVQFHPCAQVVMVAGLDNAVSLFQVDGKTNPKIQSIYFEKFPI
          TLPKGILK..KNCQHANAERPTT.R.SSV.FHPCAQ.VMV.GLDN.V.LFQVDGKTNP.IQSIY.EK.PI
Retrocopy TLPKGILK>LKNCQHANAERPTTVRISSVPFHPCAQAVMVTGLDNTVWLFQVDGKTNPRIQSIYLEKLPI

Parental  FKACFSANGEEVLATSTHSKVL-YVYDMLAGKLIPVHQVRGLKEKIVRSFEVSPDGSFLLINGVAGYLHL
          FKACFSANGE.VLATSTHS.V..YVYDMLA.KLIPV.QVRGLKEKIVRSFEVSPD.SFLLINGVAGY.HL
Retrocopy FKACFSANGEKVLATSTHSEVF>YVYDMLAEKLIPVRQVRGLKEKIVRSFEVSPDASFLLINGVAGYFHL

Parental  LSMKTKELIGSMKINGRIAASTFSSDSKKVYASSGDGEVYVWDVNSRKCLNRFVDEGSLYGLSIATSRNG
          LSMKTKELIGSMKINGR.AASTFSSDSKKVYASSGDGEVYVWDVNSRKCLNRFVDE.SLYGLS.ATSRNG
Retrocopy LSMKTKELIGSMKINGRTAASTFSSDSKKVYASSGDGEVYVWDVNSRKCLNRFVDEDSLYGLSVATSRNG

Parental  QYVACGSNCGVVNIYSQDSCLQETNPRPIKAIMNLVTGVTSLTFNPTTEILAIASEKMKEAVRLVHLPSC
          QYVACGSNCGVVNIYSQDSCL.ETNP.PIKA.MNLVTGVTSLTFNPTTEILAIASEKMKEAVRLVHLPSC
Retrocopy QYVACGSNCGVVNIYSQDSCL*ETNPKPIKATMNLVTGVTSLTFNPTTEILAIASEKMKEAVRLVHLPSC

Parental  TVFSNFP-VKKKNISLV-HTMDFSPRSGYFALGNEKGKALMYRLHHYSDF
          ..FS.FP.VKKKNISLV....DFS.RSGYFALGNEKGKALM..LHHYSDF
Retrocopy IGFSSFPVVKKKNISLV>YATDFSSRSGYFALGNEKGKALMNKLHHYSDF

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_170 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_170 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001477	1 retrocopy	retro_cpor_657,
Homo sapiens	ENSG00000011260	1 retrocopy	retro_hsap_1882,
Gorilla gorilla	ENSGGOG00000017061	1 retrocopy	retro_ggor_1379,
Myotis lucifugus	ENSMLUG00000016938	1 retrocopy	retro_mluc_2308,
Mustela putorius furo	ENSMPUG00000015582	1 retrocopy	retro_mputfur_646,
Vicugna pacos	ENSVPAG00000010164	1 retrocopy	retro_vpac_170 ,