RetrogeneDB ID: retro_vpac_49

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1235:53819..54317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL24
• Ensembl ID: ENSVPAG00000012246
• Aliases: None
• Description: ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]

Sequence

>retro_vpac_49
TTCCCTTCTCCCAGCCCATTCACAGCCATGAAGGTCGAGCTGTGCAGTTTCAGCAGGTACAAGATAGACCTAGGACATGG
GAGGTGCTATGCCAGGACCAATGGGAAGGTTTTCCAGTTTCTTAATGCAAAATGTGAGTGGGCGTTCCTTTCCAAGAGGA
ATCCTCGGCAGGTCAACTGGAATGTCCTCTACAGAAGAAAGCACAAAAAGGGACAATTGGAAGAAATTCAAAAGAAAAGA
ACTCGCCGTGCAGTCAAATTCCAGAGGGCCATAACTGGTTCATTTCTTGCTGATACAATGACCAAGAGGAATCAGAAACC
TGGAGTTTGGAAGACTCAACGAGAACAGGATCTCAGGGCTGCTAAGGCAGCCAAAAAGGCTAAGCAAGCACCTAAAAAGA
CAGCAGTGGCTGCTGCAAAGGCTCTCACAAAGGCAGCACCTAAGCAAAGGATTGTGAAGCCTGTGAAGGTTTCTGCGCCC
CAAGTAGGTGGAAAACGC

Alignment

ORF - retro_vpac_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 95.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPSLGPYAAMKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKK
          FPS..P..AMKVELCSFS.YKI..GHGR.YART.GKVFQFLNAKCE.AFLSKRNPRQ.NW.VLYRRKHKK
Retrocopy FPSPSPFTAMKVELCSFSRYKIDLGHGRCYARTNGKVFQFLNAKCEWAFLSKRNPRQVNWNVLYRRKHKK

Parental  GQSEEIQKKRTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAK
          GQ.EEIQKKRTRRAVKFQRAITG..LAD.M.KRNQKP.V.K.QREQ..RAAK.AKKAKQA.KKTA.AAAK
Retrocopy GQLEEIQKKRTRRAVKFQRAITGSFLADTMTKRNQKPGVWKTQREQDLRAAKAAKKAKQAPKKTAVAAAK

Parental  APTKAAPKQKIVKPVKVSAPRVGGKR
          A.TKAAPKQ.IVKPVKVSAP.VGGKR
Retrocopy ALTKAAPKQRIVKPVKVSAPQVGGKR

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_49 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_49 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 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000496	3 retrocopies	retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus	ENSCPOG00000019941	5 retrocopies	retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus	ENSDNOG00000003194	9 retrocopies	retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Felis catus	ENSFCAG00000003327	1 retrocopy	retro_fcat_31,
Macropus eugenii	ENSMEUG00000009177	7 retrocopies	retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus	ENSMLUG00000017005	4 retrocopies	retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta	ENSMMUG00000015059	9 retrocopies	retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica	ENSMODG00000001916	3 retrocopies	retro_mdom_675, retro_mdom_854, retro_mdom_974,
Procavia capensis	ENSPCAG00000005918	1 retrocopy	retro_pcap_192,
Pan troglodytes	ENSPTRG00000015176	2 retrocopies	retro_ptro_1214, retro_ptro_85,
Rattus norvegicus	ENSRNOG00000001611	25 retrocopies	retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sarcophilus harrisii	ENSSHAG00000008226	2 retrocopies	retro_shar_171, retro_shar_264,
Ictidomys tridecemlineatus	ENSSTOG00000014654	2 retrocopies	retro_itri_442, retro_itri_69,
Vicugna pacos	ENSVPAG00000012246	3 retrocopies	retro_vpac_49 , retro_vpac_520, retro_vpac_597,