RetrogeneDB ID: retro_vpac_12

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_14151:792..1920(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000010513
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_vpac_12
ATGGATAACGATACTGCTGCAATCGTGGTTGACAGCGGCTCCGGCATGTGCAAGGCTGGCTTCGCGGGCAACGATGCCCC
CCAGGCCGTCTTCCCCTCCGTCGTGGGACGCCCCCGGTACCAGGGCGTCATGGTAGGCATGGACCAGAAGGACTCCTATG
TAGGTAATGAGGCCCAAAGCAAGAGAGGCATCCTGACCCTCAAGTACCCCATTGAACACGGCATTGTCACCAACTGGGAT
GACATGGAGAAGATCTGGCACCACACCTTCTATAATGAGCTGCGCGTGGCCCCAGAGGAGCACCCCTTGCTGCTGACTGA
GGCCGCACTGAACCCCAAGGCCAACCGTGAGAAGATGGTTCAGATCATGTTCGAGACCTTCAACACCCCAGCCATGTACA
TGGCCATCCAGGCTGTGCTGTCCTTGTACACCTCTGGCCGCACCACTGGCATTGTGATGGACTCTGGTGATGGGGTCACT
CACACTGTGCCCACCTACGAGGGGCATGCCCTCCCCCACGCCACCCTGCATCTGGACCTGGCTGGCCGGGACCTGACGGA
CTACCTTATGAAGATCCTCATGGAACGTGGCTACAGGTTCACCACCACGGCCGAGCGGGAAATCGTGCGTGACATCAAAG
AGAAGCTCTGCTACGTCGCCCTGGACTTGGAGCAGGAGATGGCCACTGCCGCCTCCAGCTCCTCCCTGGAGAAGAGCTAT
GAGCTGCCCGATGGTCAGGTCATCACCATTGGCAGCGAGCGCTTCCGCTGCCCTGAGGCTCTCTTCCAGCCCGCTTTCCT
GGGCCTGGAAGCCTGTGGCATCCACGAGACTACCTTCAACTCCATCATGAAGTGTGACATGGACATCCGCAAGAACCTCT
ATGCCAACACGGTGCTGTCTGGCGGGACCACCATGTACCCCGGCATCACCGGCAGGATGCAGAAGGAGCTCACTGCCCTG
GCCCCCAGCACGGTGAAGGTCAAGATCATTGCGCCCTCTGAGCGCAAGTACTCCGTGTGGATGGGTGGCTCCATCCTGGC
CTCACTGCCCACCTTCCAGCAGATGTGGATCAGCAACCAAGAGTATGATGAGTTTGGTCCCTCCATCGTCCACCGCAAGT
GCTTCTAG

Alignment

ORF - retro_vpac_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLN
          GVMVGM.QKDSYVG.EAQSKRGILTLKYPIEHGI.TNWDDMEKIWHHTFYNELRVAPEEHP.LLTEA.LN
Retrocopy GVMVGMDQKDSYVGNEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPLLLTEAALN

Parental  PKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLA
          PKANREKM.QIMFETFN.PAMY.AIQAVLSLY.SGRTTGIV.DSGDGVTH.VP.YEG.ALPHA...LDLA
Retrocopy PKANREKMVQIMFETFNTPAMYMAIQAVLSLYTSGRTTGIVMDSGDGVTHTVPTYEGHALPHATLHLDLA

Parental  GRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIG
          GRDLTDYLMKIL.ERGY.F.TTAEREIVRDIKEKLCYVALD.E.EMATAASSSSLEKSYELPDGQVITIG
Retrocopy GRDLTDYLMKILMERGYRFTTTAEREIVRDIKEKLCYVALDLEQEMATAASSSSLEKSYELPDGQVITIG

Parental  NERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALA
          .ERFRCPE.LFQP.F.G.E..GIHETT.NSIMKCD.DIRK.LYAN.VLSGGTTMYPGI..RMQKE.TALA
Retrocopy SERFRCPEALFQPAFLGLEACGIHETTFNSIMKCDMDIRKNLYANTVLSGGTTMYPGITGRMQKELTALA

Parental  PSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDEAGPSIVHRKCF
          PST.K.KIIAP.ERKYSVW.GGSILASL.TFQQMWIS.QEYDE.GPSIVHRKCF
Retrocopy PSTVKVKIIAPSERKYSVWMGGSILASLPTFQQMWISNQEYDEFGPSIVHRKCF

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_12 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_12 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,