RetrogeneDB ID: retro_vpac_135

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2038:970216..971124(+)
• Located in intron of: ENSVPAG00000007809

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCM4
• Ensembl ID: ENSVPAG00000012049
• Aliases: None
• Description: minichromosome maintenance complex component 4 [Source:HGNC Symbol;Acc:6947]

Sequence

>retro_vpac_135
CTTGATTTTCTTTTTAGTTCAGCACTGACATATGGCACTCCCAGCCCGTGTAGAGAGGGAACCCCAAGCTGTGGTGTTAG
GGACACAGCCATGAGGCACAGGCCTGACCTGGGGTCTGCAGGGAAAGATCTGCAGGTGGATTTGCAGTATGAGCCAGCAA
CAGAAGATACAGTGGCCAGTGAGCAGTTTCTAAGCCAAAAACTTGTGATTTGAGGAATAGATGTAAATATGGCCACCTGC
AAAGAAAATTTTCAGAGATGTCTTTAGCATTTTCTTGACCCTCTGACTAAAGAATAAAATGTTGCCATAGATACTGCTGA
GTCTCTGTACATGCAACTGCTTGGGGAAACTAATGTTATTGAAGAGCCATTTTTAAATGTAAACTGTAAATGCATAAAGT
CATGTGACAAAAATTGGTACAGACAGCGCATCTGCTTCCCACAGGAAGTTATCCCAGCTTTTACCATGGCTGTCAGTGAG
ATCTGACTCAGTCTTTGAATAGCAGATTCGATTAGGACCATTCAATGTGTTGAAGGCAAAGAATATGAGAAACCCGAATC
TAGAAGACATCAGTCAGCTCATCACCATCAGTGGCATGGTGATCAGATGTCACGGCTGATTCCAGAGAGGCATGGGGCCT
TCCTCCGGTGCCAGGTGTGCACCCACACTGTCCTAGTGTAGATGGACCCGGTCAGATCACTGAGCCCTGCACGTGCTCGA
GCTGCCACGCCACCATGGGTGCTGGCCATGACTGCCTGGTGTTCTCTGACAAGCAAGAGTCTCCTGAAAACATGCCTGCA
GGGCAGATGCCTCGCACTGTCATCCTTTTTGCTCACAATGATATTGTTGACAAGGTTCAACTTGGGAACAGAGTGAACAT
TACAAGCATCTCTCCAGCTGTTCCTACT

Alignment

ORF - retro_vpac_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 57.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDLDVSSPLTYGTPSSRVEGTPRSGVRGTPVRQRPDLGSARKGLQVDLHSDGPAAEDIVASEQSLGQKLV
          LD...SS.LTYGTPS...EGTP..GVR.T..R.RPDLGSA.K.LQVDL....PA.ED.VASEQ.L.QKLV
Retrocopy LDFLFSSALTYGTPSPCREGTPSCGVRDTAMRHRPDLGSAGKDLQVDLQYE-PATEDTVASEQFLSQKLV

Parental  IWGTDVNVAACKESFQRFLQRFIDPLAKEEENVGIDVTEPLYMQRLGEINVIGEPFLNVNCEHIKSFDSN
          I.G.DVN.A.CKE.FQR.L..F.DPL.KE..NV.ID..E.LYMQ.LGE.NVI.EPFLNVNC..IKS.D.N
Retrocopy I*GIDVNMATCKENFQRCL*HFLDPLTKE*-NVAIDTAESLYMQLLGETNVIEEPFLNVNCKCIKSCDKN

Parental  LYRQLTCYPQXVIPAFTMAVSE-SDSVFE-QIRLGPFNVLKAKNMRNPNLEDISQLITISGMVIRCHG-L
          .YRQ..C.PQ.VIPAFTMAVSE.SDSVFE.QIRLGPFNVLKAKNMRNPNLEDISQLITISGMVIRCHG.L
Retrocopy WYRQRICFPQEVIPAFTMAVSE>SDSVFE*QIRLGPFNVLKAKNMRNPNLEDISQLITISGMVIRCHG<L

Parental  IPERHGAFLRCQVCTHTVLV-MDG--QITEPCTCSSCHATMGAGHDCPAF-NKQESPENMPAGQMPRTVI
          IPERHGAFLRCQVCTHTVLV..DG..QITEPCTCSSCHATMGAGHDC..F..KQESPENMPAGQMPRTVI
Retrocopy IPERHGAFLRCQVCTHTVLV<VDGPGQITEPCTCSSCHATMGAGHDCLVFSDKQESPENMPAGQMPRTVI

Parental  LFAHNDIVDKVQLGNRVNITSISPAVPT
          LFAHNDIVDKVQLGNRVNITSISPAVPT
Retrocopy LFAHNDIVDKVQLGNRVNITSISPAVPT

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_135 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_135 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017021	1 retrocopy	retro_btau_1489,
Monodelphis domestica	ENSMODG00000010213	1 retrocopy	retro_mdom_1561,
Rattus norvegicus	ENSRNOG00000001833	1 retrocopy	retro_rnor_1549,
Vicugna pacos	ENSVPAG00000012049	1 retrocopy	retro_vpac_135 ,