RetrogeneDB ID: retro_vpac_50

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1243:46924..47968(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSVPAG00000007543
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_vpac_50
GATGGTGAGACCATTCTGAAAGGCCTCCAGTCCATTTTCCAGGAGAAGGGGATGACGGAGTCGGTGCACACCTGGCAGGA
CCATGGCTATTTAGCGACCTACATAAACAAAAACGGCAGCTTTGCCAATTTGAGAATTTACCCACATGGACTGGTGTTGC
TGGACCTTCAGAGTTACGACGGGGATGCGCAAGGCAAAGAAGTTGACAGTCTTTTGAACAAAGTAGAAGAAAGAATGAAA
GAATTGAGTCAGGGCAGTACTGAGCGGGTGAAGCGCTTACCACCCATAGTTCGAGGAGGGGCCGTTGACAGATACTGGCC
CACTGCCGATGGCCGTCTGGTTGAGTACGACATAGATGAAGTGGTGTATGATGAAGACTCACCTTACCAGAACATTAAAA
TTTTACACTCGAAACAATTTGGAAACATTCTCATCCTTAGTGGGGATGTTAATTTGGCAGAAAGTGACTTGGCGTATACC
CGGGCCATCATGGGCAGTGGCAAGGAAGATTACACCGGCAAAGATGTACTCATTCTGGGAGGTGGAGATGGGGGCATATT
ATGTGAAATAGTCAAACTGAAACCAAAGATGGTCACTATGGTAGAGATTGACCAAATGGTGATTGACGGATGTAAGAAAT
ACATGCGAAAAACGTGTGGCGATGTCTTAGACAATCTTAAAGGAGACTGCTATCAGGTTCTAATAGAAGACTGTATTCCA
GTCCTGAAGAGGTACGCCAAAGAAGGGAGAGAGTTTGATTATGTGATTAATGATTTGACAACTGTTCCAATCTCCACATC
TCCAGAAGAAGATTCCACATGGGAGTTTCTCAGACTGATTCTTGACCTCTCAATGAAAGTATTGAAACAGGATGGGAAAT
ATTTTACACAGGGGAACTGTGTCAATTTGACGGAAGCCCTGTCACTCTATGAAGAACAGCTGGGGCGCCTGTATTGTCCT
GTGGAATTCTCGAAGGAGATTGTCTGTGTCCCTTCATACTTGGAATTGTGGGTATTTTACACTGTTTGGAAGAAAGCTAA
ACCT

Alignment

ORF - retro_vpac_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.14 %
• Parental protein coverage: 87.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGETILKGLQSIFQEKGMTESVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVDS
          DGETILKGLQSIFQEKGMTESVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVDS
Retrocopy DGETILKGLQSIFQEKGMTESVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVDS

Parental  LLNKVEERMKELSQDSTERVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQF
          LLNKVEERMKELSQ.STERVKRLPPIVRGGA.DRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQF
Retrocopy LLNKVEERMKELSQGSTERVKRLPPIVRGGAVDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQF

Parental  GNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDG
          GNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDG
Retrocopy GNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDG

Parental  CKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLI
          CKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLT.VPISTSPEEDSTWEFLRLI
Retrocopy CKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTTVPISTSPEEDSTWEFLRLI

Parental  LDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP
          LDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP
Retrocopy LDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP

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_50 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_50 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50 ,