RetrogeneDB ID: retro_vpac_601

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_6463:31395..32159(-)
• 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_601
AACAATGTAGACATTGACAACAAAGAACAGTCTGAACTTGATCAACATTTGGCTGATGTTGAAAAAGTAGAAAAAGAAAC
AAAAATTGAAGCATGCCAGCTGACTGTTCAAATGCAGCAAAATCCTCAGATTCTTGCAGTCCTTCAAGAAAGACCTGATG
GTCTGGTAGAAACATCAACAGGATACATTGAAAACTTGCCTAGGGTAGTTATAAGATGAGCAGTGCTCTCGAAAACCTTC
AAGTTAAATGTACACAGACAACAGCCAAATTCTATGAGGAAGTTCATGATCTTGAAAGAAAGTATGCTGTTCTCTCTCAG
CCTCTCTATTTATAAGCGATTTAAGATCATCAATGCAATTTATGAACCTATAGAAGAAGAATGTGAATGGAAACCAGAAT
AGGAAGGTGAAATTTTGGAGGAGTTGAAAAAAAAGGCCAACATTGAAGATGAGGAAAAAGATAAAAAGAAAGAAGACCAC
AAGGAAATTCCTGAATTTTGGTTGACTGTTTTTAAGAATGTTGACTTACTTAGTGGTATGTTTTAGGAACATGATAAACT
TATTATGAAGCATTTAAAAGATATTAAAGGGAAGTTTTTAGCTGCAGGCCAGCCTATGAGTTTTGAATTTCACTTTGAAC
CCAGTGAATATTTCACAAATGAAGTGTTGACAAAGACATATAGGATGGAGTCAGAACCAGATGATTCTGATCTCTTTTCT
TTTGATGGCCCAAAAATCATGGGTTGTAAAGGTGCCAGATAGAT

Alignment

ORF - retro_vpac_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.92 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESLPRVV
          .N.......Q...D......E....ETKI.A.QLTVQM.QNPQILA.LQER.DGLVET.TGYIE.LPRVV
Retrocopy NNVDIDNKEQSELDQHLADVEKVEKETKIEACQLTVQMQQNPQILAVLQERPDGLVETSTGYIENLPRVV

Parental  KR-RVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLF-DKRFEIINAIYEPTEEECEWKPDEEDEI
          .R....AL.NLQVKC.Q..AKFYEEVHDLERKYAVL.QPL...KRF.IINAIYEP.EEECEWKP..E.EI
Retrocopy IR<MSSALENLQVKCTQTTAKFYEEVHDLERKYAVLSQPLY>YKRFKIINAIYEPIEEECEWKPE*EGEI

Parental  SEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSF
          .EEL...A.IEDE.KD..KED.K.IPEFWLTVFKNVDLLS.M..EHD..I.KHLKDIK.KF..AGQPMSF
Retrocopy LEELXXXANIEDEEKDKKKEDHKEIPEFWLTVFKNVDLLSGMF*EHDKLIMKHLKDIKGKFLAAGQPMSF

Parental  VLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTG-CQID
          ..EFHFEP.EYFTNEVLTKTYRM.SEPDDSD.FSFDGP.IMGC.G.CQID
Retrocopy --EFHFEPSEYFTNEVLTKTYRMESEPDDSDLFSFDGPKIMGCKG<CQID

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_601 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_601 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 ,