RetrogeneDB ID: retro_vpac_134

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2028:59043..59342(+)
• Located in intron of: ENSVPAG00000011449

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSVPAG00000005953
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_vpac_134
ACAGCCTCCAAGAAAACTAGGCTGTCCCAACCCCCTGGTAATAGATTTGTTTACCTTTATACCAAGAAGCTTAGGAAAGC
ACCAAAACCCTCATGTGAAATGTGCCCAAGCCAAATTTAAGAAGTTGGTTTGGTGAGACCCAAAGTATCTAGAGGTTTTC
TGAAATGAAACATGTCAGCAGGGCCTGTGGTGGCTCTGTGTCTGCTAAGTGTGTCCGTGACCAGATCACACATGCTTTCC
TCACCGAGGAGCTGAAAATCCTCGTGAAAGTGTTGAAGGCACAAGCAGAGTCAGAAAGG

Alignment

ORF - retro_vpac_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.75 %
• Parental protein coverage: 86.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TASNKTRLARTPGNRIFYLYTKK-GKAPKSACGLCPGRLRGVRAVRPKV-LMRLSKTKKHVSRAYGGSMC
          TAS.KTRL...PGNR..YLYTKK..KAPK..C..CP.....V..VRPKV...R.S..K.HVSRA.GGS..
Retrocopy TASKKTRLSQPPGNRFVYLYTKKLRKAPKPSCEMCPSQI*EVGLVRPKV<I*RFSEMK-HVSRACGGSVS

Parental  AKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQK
          AKCVRD.I..AFL.EE.KI.VKVLKAQA.S..
Retrocopy AKCVRDQITHAFLTEELKILVKVLKAQAESER

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_134 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_134 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 14 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Pteropus vampyrus	ENSPVAG00000005914	9 retrocopies	retro_pvam_1078, retro_pvam_1114, retro_pvam_1394, retro_pvam_189, retro_pvam_192, retro_pvam_225, retro_pvam_264, retro_pvam_312, retro_pvam_361,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Vicugna pacos	ENSVPAG00000005953	9 retrocopies	retro_vpac_134 , retro_vpac_280, retro_vpac_309, retro_vpac_414, retro_vpac_421, retro_vpac_430, retro_vpac_514, retro_vpac_537, retro_vpac_84,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,