RetrogeneDB ID: retro_vpac_138

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2054:324047..324313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSVPAG00000001801
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_vpac_138
AAATGCCATGAACATACAGAAATCCTTACAGTAAATGGAGAGTTACTATTTTTCAAAGAGAAGGGCCTTTTTATCCAACC
CTAAGATTACTTCACAAATATCCTTTTATCTTGTCACAACAGCAGGTTGATAAAGGAGCCATCAGATTTGTACTCACTGG
AGCAAATTTCATACATCCAGGCTTAACCTCTCTTGGAGCTAAACTTTACTCTGCTGCAGTAGATACCATCGTTGCAATCA
CGGCAGAAGGAAAACAGCGTGTGTTG

Alignment

ORF - retro_vpac_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.02 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RCHEHIEILTVNGELLFFRQREGPF-YPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAK
          .CHEH.EILTVNGELLFF....G.F.YPTLRLLHKYPFIL..QQVDKGAI.FVL.GAN...PGLTS.GAK
Retrocopy KCHEHTEILTVNGELLFFKEK-GLF<YPTLRLLHKYPFILSQQQVDKGAIRFVLTGANFIHPGLTSLGAK

Parental  LYPAAVDTIVAIMAEGKQHAL
          LY.AAVDTIVAI.AEGKQ..L
Retrocopy LYSAAVDTIVAITAEGKQRVL

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_138 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_138 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138 ,