RetrogeneDB ID: retro_tbel_1199

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4078:559271..559643(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS14
• Ensembl ID: ENSTBEG00000003335
• Aliases: None
• Description: mitochondrial ribosomal protein S14 [Source:HGNC Symbol;Acc:14049]

Sequence

>retro_tbel_1199
ATGGCAGTCTCCATGCTAGGCTCACTGCTGTGGACATTCCGGCAGATGGTTCCTTCATCAGCCCCAGGCCAAGTTGGAGG
TTACTATGTAGACTAGAAAACGTCGCATGATGTGAAGAGATGAAAAATGGCCTATGACTATGCTGATGAAAGGCTATGGA
TCAACTCGCTTAGGAAGAATACCTTTTTGCCAAAAGATCTTCAGGATGTGGCTGATGAAGAAATTGCTGCCCTTCAGAGC
TGTCCGGTCAGAATCCGAAATCAGTGTGTCATGACATCCCGTCCACGTGGCGTGAAGCGGCACGGGAGGCTGAGTCGCAT
CGTCTTCCGTCACTTAGCCGACCATGGGCAGCTCTCTGGAGTCCAGCGAGCA

Alignment

ORF - retro_tbel_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.92 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAFMLGSLLRTFRQMVPSSASGQVRGYYVDWKMLRDVKRRKMAYDYADERLRINSLRKNTILPKDLQDM
          MA..MLGSLL.TFRQMVPSSA.GQV.GYYVD.K...DVKR.KMAYDYADERL.INSLRKNT.LPKDLQD.
Retrocopy MAVSMLGSLLWTFRQMVPSSAPGQVGGYYVD*KTSHDVKR*KMAYDYADERLWINSLRKNTFLPKDLQDV

Parental  ADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQLSGVQRA
          ADEEIAAL...SCPVRIRN.CVMTSRPRGVKR..RLSRIVFRHLADHGQLSGVQRA
Retrocopy ADEEIAAL--QSCPVRIRNQCVMTSRPRGVKRHGRLSRIVFRHLADHGQLSGVQRA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1199 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1199 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001109	1 retrocopy	retro_btau_149,
Callithrix jacchus	ENSCJAG00000008986	1 retrocopy	retro_cjac_136,
Mus musculus	ENSMUSG00000058267	1 retrocopy	retro_mmus_463,
Oryctolagus cuniculus	ENSOCUG00000026497	1 retrocopy	retro_ocun_34,
Tupaia belangeri	ENSTBEG00000003335	1 retrocopy	retro_tbel_1199 ,