RetrogeneDB ID: retro_tbel_3939

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_4179:66134..66576(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM2
• Ensembl ID: ENSTBEG00000004587
• Aliases: None
• Description: phosphoglycerate mutase 2 (muscle) [Source:HGNC Symbol;Acc:8889]

Sequence

>retro_tbel_3939
GCCAAGCACGGGGAGGCGCAGGTGAAGATCTGGAGACGTTCCCACGATGTCCGCTGACCCCAATGGGGCACAACTGCCCC
TTCTACAGCAACGTCAGTAAGGATCGCAGGTGTGCAGACCTCACCGGATCAACTGCCCTCCTGTGAGCGTCTGAAGGACA
CGGTGGCCAGAGCTCTGCCCTTCTGGAATGAGGAAACCATTCCCCAGATCCAGGAGAGGAAACGCGTGCTGATCACAGCC
CACGGCAACAGCCTGCGGGCCATCGTCAAGCACCTGGACGGTCTCTCTGAAGGGGCTATCGTGGGGCTGAACTGCCGACA
GGTATCCCCATTGCCTATGAGTTGGACAAGAACCTGAAGCCCATCAAGCCCATGTAGTTCCTGGGGGATGAAGAGACCGT
GCTAAAGCCATGGAAGCTGTGGCTGCCCAGGGCAAGGCCAAG

Alignment

ORF - retro_tbel_3939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 58.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKHGEEQVKIWRRSFDIPPPPMDEKHPYYSTISKERRYAGLK--PGELPTCESLKDTIARALPFWNDEIA
          AKHGE.QVKIWRRS.D...P......P...T.....R.AG....P..LP.CE.LKDT.ARALPFWN.E..
Retrocopy AKHGEAQVKIWRRSHDVR*PQWGTTAPSTAT---SVRIAGVQTSPDQLPSCERLKDTVARALPFWNEETI

Parental  PQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELN-LPTGIPIVYELDQALKPTKPMRFLGDEETV-R
          PQI...KRVLI.AHGNSLR.IVKHL.G.S..AI..LN.LPTGIPI.YELD..LKP.KPM.FLGDEETV..
Retrocopy PQIQERKRVLITAHGNSLRAIVKHLDGLSEGAIVGLN<LPTGIPIAYELDKNLKPIKPM*FLGDEETV<A

Parental  KAMEAVAAQGKAK
          KAMEAVAAQGKAK
Retrocopy KAMEAVAAQGKAK

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_3939 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3939 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 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024480	1 retrocopy	retro_dnov_34,
Macropus eugenii	ENSMEUG00000012920	8 retrocopies	retro_meug_1044, retro_meug_1303, retro_meug_1636, retro_meug_1838, retro_meug_202, retro_meug_2152, retro_meug_251, retro_meug_945,
Otolemur garnettii	ENSOGAG00000006713	1 retrocopy	retro_ogar_164,
Procavia capensis	ENSPCAG00000002181	1 retrocopy	retro_pcap_13,
Rattus norvegicus	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939 ,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,