RetrogeneDB ID: retro_vpac_355

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_11589:10364..11272(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000010621
• Aliases: None
• Description: None

Sequence

>retro_vpac_355
ATCGTCACCAACTGGGAGGACATGGAGAAGATCTGACACCACACCTTCTACAACAAGCTGCATGTGGCCCCTGAGGAGCA
CCCCGTGCTGCTGACCAAGGCCCTGCTGAACCCCAAGGCCAACCATGAGAAGATGACCCAGATCATGTTCGGGACTTTCA
ACACCCCAGCCATGTATGTGGCCATCCAGGCTGTGCTGTCCCTGTACTCCTCTGGCAGCACCACTGGCATCATGATGGAT
TCCGGTGATGCGGTCACTCACACTGTGTCCATCTACAAGGTGTAAGCCATCCCCCACGCCATCATGCGTCTGGACCGGCT
GGCCAGGACCTGACGGACTACCTCACGAAGAGCCACACGAAGCGTGGCTACAGGTTCACCACTACAGCTGAGTGGGAAAT
TACACGTGACATCGAGGAGAAGCTCTGCCGTGTTGCCCGGGACTTCCAGCAGGAGATGGCCACCGCCACCTGCAGCGCCT
TCCTGGAGAAGAGCTACGAGCTGCCTGACAATCAGTTCATCACCACCGGCAACGAGCGCTTCTGCTGCCCCAAAGTTCTC
TTCCAGCCCTCATTCCTGGGCATGGACCCTCTGGCAACCACGAGACTACCTTCAACTCCATCGTGAAATGTGACGTCAAC
GTCTGCAAGGACCTCTATGCTAACACGATGCTATCTGGTGGGACTACCGTGTATCCTAGCATTACCGACGGGATGCAGAA
GGAGTTCACTGCCTTGGCTCCCAGCACGAAGAAGATGAAGATCACTGCACTCCCCTCTTCCCCAGCGCAAGTACTCCATG
TGGATCTGCGGCTCCATCCTGGCCTCATTGTCCACCTTCCAGCAGATGTGGGTCAGCAAGCAGAAGTACAACGAGTCCGG
CCCTTCCACTGCCCACCGCAAATGCTTC

Alignment

ORF - retro_vpac_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.55 %
• Parental protein coverage: 90.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYA
          I.TNW.DMEKI.HHTFYN.L.VAPEEHP.LLT.A.LNPKAN.EKMTQIMF.TFN.PAMYVAIQAVLSLY.
Retrocopy IVTNWEDMEKI*HHTFYNKLHVAPEEHPVLLTKALLNPKANHEKMTQIMFGTFNTPAMYVAIQAVLSLYS

Parental  SGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL-AGRDLTDYLMKILTERGYSFVTTAEREIVRDIK
          SG.TTGI..DSGD.VTH.V.IY...A.PHAIMRLD..AG.DLTDYL.K..T.RGY.F.TTAE.EI.RDI.
Retrocopy SGSTTGIMMDSGDAVTHTVSIYKV*AIPHAIMRLDR<AGQDLTDYLTKSHTKRGYRFTTTAEWEITRDIE

Parental  EKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMES-AGIHETTYNSI
          EKLC.VA.DF..EMATA..S..LEKSYELPD.Q.IT.GNERF.CP..LFQPSF.GM....G.HETT.NSI
Retrocopy EKLCRVARDFQQEMATATCSAFLEKSYELPDNQFITTGNERFCCPKVLFQPSFLGMDP<SGNHETTFNSI

Parental  MKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPST--MKIKIIAP-PERKYSVWIGGSILASL
          .KCD....KDLYAN..LSGGTT.YP.I.D.MQKE.TALAPST..MKI......P.RKYS.WI.GSILASL
Retrocopy VKCDVNVCKDLYANTMLSGGTTVYPSITDGMQKEFTALAPSTKKMKITALPS>PQRKYSMWICGSILASL

Parental  STFQQMWISKQEYDEAGPSIVHRKCF
          STFQQMW.SKQ.Y.E.GPS..HRKCF
Retrocopy STFQQMWVSKQKYNESGPSTAHRKCF

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_355 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_355 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 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000005463	1 retrocopy	retro_meug_970,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355 , retro_vpac_651,