RetrogeneDB ID: retro_tbel_1139

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3926:5544..6019(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000010617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSTBEG00000012320
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_tbel_1139
CTCTATTATCAAGTCCTAAATTTCAAAATGATTGTCTCTTCAACACTACTGATCTGGAAGGGGTTAATGGTAATAACTGG
AAGTGAAAGTCCAATTATAGTGATGCTCAGTGGCAGCACGCAACCTGCATTTCATAAAGGTGATCTCTTCCTAGCAAATC
GAGTTGAAGATCCTGTCTGAGTGGGAGAAATTGTCATTGTTTAGGATAGAAGGAAGAGAGATTCCTATAGTTCACTGAGT
CCTGAAGATTCATGAAAAGTAAAATGGGCATATTAAGTTTTTAGCCAAAGGCTATAATAACACAGTGGATGACCGAGGTG
TGTATAAACAAGGACAACCCTGGCTAGAGAAAAAAGATGTCGTGGGCAGAGCCAGAAGATTCGTTCCTTGTATTGGAATT
GTGACGATCCTCATAAATGACTATCCTAAATTTAAGTATGTAGTACTGTTTTTGCTGCATTTATTTGTGCTGGTC

Alignment

ORF - retro_tbel_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 97.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLTNRVEDPIRVGEIVV-FR
          LYYQVLNF.MIVSS.L.IWKGLMVITGSESPI.V.LSGS..PAFH.GDL.FL.NRVEDP..VGEIV..FR
Retrocopy LYYQVLNFKMIVSSTLLIWKGLMVITGSESPIIVMLSGSTQPAFHKGDL-FLANRVEDPV*VGEIVI>FR

Parental  IEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVGRARGFVPYIGIVTILM
          IEGREIPIVH.VLKIHEK.NGHIKFL.KG.NN.VDDRG.YKQGQ.WLEKKDVVGRAR.FVP.IGIVTIL.
Retrocopy IEGREIPIVH*VLKIHEK*NGHIKFLAKGYNNTVDDRGVYKQGQPWLEKKDVVGRARRFVPCIGIVTILI

Parental  NDYPKFKYAVLFLLGLFVLV
          NDYPKFKY.VLFLL.LFVLV
Retrocopy NDYPKFKYVVLFLLHLFVLV

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_1139 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1139 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Erinaceus europaeus	ENSEEUG00000015328	2 retrocopies	retro_eeur_314, retro_eeur_412,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Macaca mulatta	ENSMMUG00000011486	1 retrocopy	retro_mmul_2343,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Ictidomys tridecemlineatus	ENSSTOG00000019948	1 retrocopy	retro_itri_206,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139 , retro_tbel_2280, retro_tbel_745,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,