RetrogeneDB ID: retro_vpac_353

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_11451:5353..5963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSVPAG00000010259
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_vpac_353
CAGCTAGCCAGTGCCAGAAACAGAAGACTGGCCCAGCAGATGGAGAACAGACCCTCTGTCCAGGCAGCATTAAAACTTAA
GCAAAAGAGCTTAAAGCAGCACCTGGGTAAGAGTAACATCCAGGCACATTTAGGCTGACCCATAGGGGCCCTGGCCAGGG
GAGCAATCAATGGATGAGGCCTGCCCATAATCCAGAGAGCATTGCTCAGAGGAGGACTACGTGGGGGATGTGCCACAAGA
ACCCTACTTAGGGGCGGGATGTCGCTCTGAGGTCAAAACCTGCTCCAAGGTGGAAGAGCCATAGCTCCCAGAATGGCTTA
AGAAGAGGTGGTGTTCGAGGTTGTCGAGGTCCTGGGAGAGGGGGCCTAGAGCGTGGAGCTGTGGGTCGTGGTGGAATCGG
TGGTAGAGGTCGGGGTATGATAGGTCGGGGAAGAGGGGGCTTTAGAGGCCGAGGCTGAGGCCGTGGACGAGGGAGAGGTG
CCCTTGCTTACCCTGTACTGACCAAGGAGCAGCTGGACAACCAATTGGTTGCATACATGTCAAAACAAAAGGACACCTGG
ATGCTAAGTTGGATGCCTATATGGCACAGGCAGATCCTGAAACTAATGAC

Alignment

ORF - retro_vpac_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 81.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLASARNRRLAQQMENRPSVQAALKLKQ-SLKQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLPR
          QLASARNRRLAQQMENRPSVQAALKLKQ.SLKQ.LGKSNIQA.LG.PIGALARGAI.G.GLPIIQR.L.R
Retrocopy QLASARNRRLAQQMENRPSVQAALKLKQKSLKQHLGKSNIQAHLG*PIGALARGAING*GLPIIQRALLR

Parental  GGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRM-GLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRG
          GGLRGG.ATRTLLRGGMSL.GQNLL.GGRA.APRM.GLRRGGVRG..GPGRGGL.RGA.GRGGIGGRGRG
Retrocopy GGLRGGCATRTLLRGGMSL*GQNLLQGGRAIAPRM<GLRRGGVRGCRGPGRGGLERGAVGRGGIGGRGRG

Parental  MIGRGRGGFGGRGRGRGRGRGALARPVLTKEQLDNQLDAYMS-KTKGHLDAELDAYMAQTDPETND
          MIGRGRGGF.GRG.GRGRGRGALA.PVLTKEQLDNQL.AYMS.KTKGHLDA.LDAYMAQ.DPETND
Retrocopy MIGRGRGGFRGRG*GRGRGRGALAYPVLTKEQLDNQLVAYMS<KTKGHLDAKLDAYMAQADPETND

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_353 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_353 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282, retro_lafr_656,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353 ,