RetrogeneDB ID: retro_vpac_74

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1548:49334..50665(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLMH
• Ensembl ID: ENSVPAG00000003571
• Aliases: None
• Description: bleomycin hydrolase [Source:HGNC Symbol;Acc:1059]

Sequence

>retro_vpac_74
CTGAATACGGAGAAGGTAGCTGCTCTGCTTCAGAAACTGAATTCTGACCCTCAGTTCGTCCTGGCTCAGAATGTCGGCAC
CACCCACGCCCTGCTGGGCATCTGCCTGAAGAGGGCCACGGCCCAGGGTGCGCAGCATGTGTTCCAGCCCAATGTGCATC
AGGAAGGCAAGCCAGCCACCAACCAGAAGAGCTCAGGGAGATGCTGGGTCTTTTCTTGTCGGAATGTTATGAGACGTCCA
TTCATGAGAAAATTAAATATTGAGGAATTTGAGTTTATTCAGTCTTACCTCTTTTTCTGGGGCAAGGTTGAACACTGTTA
CTTCTTCTTAAACGCCTTTGTGGACACAGCCCAGAACAAGGAGCCTGAGGATGGTAGGCAGGTGCAGTATTTGCTTACAA
ATCCTGCAAATGATGGTGGCCAATGGGATATGCTTGTCAATATTGTTGAAAAATATGGTGTTGTCCCTAAGAAATGCTTC
CCTGACTCTTACACAACAGAGGCAACCAGAAGGATGAATGATATTCCGAGTCACAAGATGAGAGAATTCTGTATACGACT
ACGGAACCTGGTACACAGTGGAGCAACCAAAGGAGAGATCTCAGCCACACAGGACGTCATGGTGGAGGAGATACTCAGAG
TGGTGTGCATCTGTTTGCGTAGTCCACCAGAGACGTTCACCTGGCAGTATCGAGACAAGGATAAAAACTATCAGAAGATG
GGCCCCCTAACACCCTTGCAGTTTTACAGGGAACATGTCAAGCCACTCTTCAACATGGAAGATAAGATTTGTTTAGTGAA
TGACCCTCAGCCCAGCACAAGTACAACAAACTTTACATGGTGGACTACTTAAGCAATATGGTTGGAAGGAGAAAAACTCT
ATATACCAACCAACCCATTGACTTCTTGAAAAAGATGGTTGCTGCCTCCATCAAAGATGGAGAGGCTGTGTGGTTTGGCT
GTGATGTTGGAAAACACTTCAATAGCAAGCTGGGCCTCAGTGACATGAATGCCTATGACCATGAGTTAGTGTTTGGTGTC
TCCATGAAGAACATGAATAAAGCTGAGAGGTTGACTTTTGGTGAGTCACTCATGACCCACGCCATGACCTTCACTGCTGT
CTCAGAGAAGGATGATCAGGCTGGTAGTTTCCTGAAATGGAGAGTAGAAAATTCATGGGGTGAAGACCATGGCCATAAAG
GTTACCTGTGCATGACAGAGGAGTGGTTCTGTGAATATGTTTACGAGGTGGTGGTGGACAAGAAGCATGTCCCTGGAGAG
GTGCTGGCCATGCTAGAGCAGGAGCCCATCATCCTGCCAGCCTGGGACCCC

Alignment

ORF - retro_vpac_74 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNTEKVAALLQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQGAQHVFQHAVHQEGKPVTNQKSSGRCWI
          LNTEKVAALLQKLNSDPQFVLAQNVGTTH.LL.ICLKRAT.QGAQHVFQ..VHQEGKP.TNQKSSGRCW.
Retrocopy LNTEKVAALLQKLNSDPQFVLAQNVGTTHALLGICLKRATAQGAQHVFQPNVHQEGKPATNQKSSGRCWV

Parental  FSCLNVMRLPFMRKLNIEEFEFSQSYLFFWDKVERCYFFLNAFVDTAQKKEPEDGRLVQYLLTNPANDGG
          FSC.NVMR.PFMRKLNIEEFEF.QSYLFFW.KVE.CYFFLNAFVDTAQ.KEPEDGR.VQYLLTNPANDGG
Retrocopy FSCRNVMRRPFMRKLNIEEFEFIQSYLFFWGKVEHCYFFLNAFVDTAQNKEPEDGRQVQYLLTNPANDGG

Parental  QWDMLVNIVEKYGVVPKKCFPESYTTEATRRMNDILNHKMREFCIRLRNLVHSGATKGEISATQDVMMEE
          QWDMLVNIVEKYGVVPKKCFP.SYTTEATRRMNDI..HKMREFCIRLRNLVHSGATKGEISATQDVM.EE
Retrocopy QWDMLVNIVEKYGVVPKKCFPDSYTTEATRRMNDIPSHKMREFCIRLRNLVHSGATKGEISATQDVMVEE

Parental  IFRVVCICLGNPPETFTWEYRDKDKNYQKFGPITPLKFYREHVKPLFNMEDKICLVNDPRP-QHKYNKLY
          I.RVVCICL..PPETFTW.YRDKDKNYQK.GP.TPL.FYREHVKPLFNMEDKICLVNDP.P.QHKYNKLY
Retrocopy ILRVVCICLRSPPETFTWQYRDKDKNYQKMGPLTPLQFYREHVKPLFNMEDKICLVNDPQP<QHKYNKLY

Parental  TVDYLSNMVGGRKTLYNNQPIDFLKKMVAASIKDGEAVWFGCDVGKHFNSKLGLSDMNVYDHELVFGVSM
          .VDYLSNMVG.RKTLY.NQPIDFLKKMVAASIKDGEAVWFGCDVGKHFNSKLGLSDMN.YDHELVFGVSM
Retrocopy MVDYLSNMVGRRKTLYTNQPIDFLKKMVAASIKDGEAVWFGCDVGKHFNSKLGLSDMNAYDHELVFGVSM

Parental  KNMNKAERLTFGESLMTHAMTFTAVSEKDDQAGSFLKWRVENSWGEDHGHKGYLCMTDEWFSEYVYEVVV
          KNMNKAERLTFGESLMTHAMTFTAVSEKDDQAGSFLKWRVENSWGEDHGHKGYLCMT.EWF.EYVYEVVV
Retrocopy KNMNKAERLTFGESLMTHAMTFTAVSEKDDQAGSFLKWRVENSWGEDHGHKGYLCMTEEWFCEYVYEVVV

Parental  DRKHIPEEVLAVLEQEPIVLPAWDP
          D.KH.P.EVLA.LEQEPI.LPAWDP
Retrocopy DKKHVPGEVLAMLEQEPIILPAWDP

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_74 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_74 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021370	1 retrocopy	retro_btau_1510,
Callithrix jacchus	ENSCJAG00000013781	1 retrocopy	retro_cjac_2998,
Cavia porcellus	ENSCPOG00000005048	1 retrocopy	retro_cpor_896,
Macropus eugenii	ENSMEUG00000008938	1 retrocopy	retro_meug_2120,
Rattus norvegicus	ENSRNOG00000003563	1 retrocopy	retro_rnor_566,
Tursiops truncatus	ENSTTRG00000016341	1 retrocopy	retro_ttru_1915,
Vicugna pacos	ENSVPAG00000003571	1 retrocopy	retro_vpac_74 ,