RetrogeneDB ID: retro_vpac_435

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_187362:490..1190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSVPAG00000007290
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_vpac_435
ATGGCAGACATTGGCAACAAAGAACGGTCTCAACTTGATCAAGGTCTGGATGATGCTAGAGAAGTAGAGGAGGGAGAAAC
TGGTGAAGAAACAAAAATCAAAGCGCTGACTGTTCAGATGATGCTAAATTCTCAGACGCCCACAGCCATTCAAGAAAGAC
TTGATGGCCTGGCAGAAACACCAGCAGGATCCACTGAAAGCTTGCCTAGGATAGTTAAAACACGAGTGAATGCTCTCAAA
AACCTCCACGTTAAATGTGCACAGACAGAAGCCAAATTCCGTGAGGAAGTTCATAATCTTGAAAGAAAGAATGCTAGTCT
CCATCAGTCTCTATTTGATGAGCGATTTGAGATTATTAATGCAATTTATAGACCTATGGAAGAACGTGAATGGAAACCAG
ATGAGGAAAATGAAATTTCAGAGGAGCTGAAAGAAAAGGCCAAGGTTGGAGATGAGAAAAAAGATGAAGAAAAAGACGAC
CCCAAGGGAATTCCTGAATTTTCAGTTGACTGTTTTTAAGAATGTTGACTTGCTCAATGATCTGGTTCAGGAACTCGATG
GACCTATCCTGAAGCACTTGAAAGATACTAAAGGGAGGTTCTCAGATGCCAGCCAGCCTGCGAGTTTTGTCTTAGAATTT
CACTTTGAACCCAATGAATATTTCACAAATGAAGTGTTGACAAAGATATATAGGATGAGG

Alignment

ORF - retro_vpac_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 60.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADI.NKE.S.LDQ.LDD..EVEE.ETGEETKIKA..LTVQMM.N.Q...A.QERLDGL.ETP.G..ESL
Retrocopy MADIGNKERSQLDQGLDDAREVEEGETGEETKIKA--LTVQMMLNSQTPTAIQERLDGLAETPAGSTESL

Parental  PRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEED
          PR.VK.RVNALKNL.VKCAQ.EAKF.EEVH.LERK.A.L.Q.LFD.RFEIINAIY.P.EE..EWKPDEE.
Retrocopy PRIVKTRVNALKNLHVKCAQTEAKFREEVHNLERKNASLHQSLFDERFEIINAIYRPMEER-EWKPDEEN

Parental  EISEELKEKAKIEDEKKDEEKEDPKGIPE-FWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQP
          EISEELKEKAK..DEKKDEEK.DPKGIPE.F.LTVFKNVDLL.D.VQE.D.PILKHLKD.K..FSDA.QP
Retrocopy EISEELKEKAKVGDEKKDEEKDDPKGIPE>FQLTVFKNVDLLNDLVQELDGPILKHLKDTKGRFSDASQP

Parental  MSFVLEFHFEPNEYFTNEVLTKTYRMR
          .SFVLEFHFEPNEYFTNEVLTK.YRMR
Retrocopy ASFVLEFHFEPNEYFTNEVLTKIYRMR

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_435 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_435 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 15 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435 , retro_vpac_441, retro_vpac_601,