RetrogeneDB ID: retro_tbel_4243

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_73104:4065..4474(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000000221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSTBEG00000016171
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_tbel_4243
ATGGCTCCTGCAAAGCTCACAGCCGGCAAATCCACGGGTGGTAAAGCAGCCAGGAAGCAACTGGCTACAAAAGCCGTTTG
CACGAGTGCGCCCTCTACCGGTAGGGTGAAGAAACCTCATTGTTACTAGCCCGAGTCTGTGGCACTGGGTAAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTCATCTGCAAACTTCCTTTCCAGAGTCTGCTGCGAAAAATTGCTCAGGACTTCAAC
ACCAAATCTGCACTTCCAGAGCGCAGCTATTGGTGCTTTGCAAGATACAAATGAGGCCTATTTGGTTGGCCTTTCTGAAG
ATACCAACCTGCGTGCTATCTATGCCAAACGTGTACCAATGATGCCAAAAGACAGCCAGCTAGCACGCTGCATACGGGTA
GAACGTGCT

Alignment

ORF - retro_tbel_4243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MA..K.TA.KSTGGKA.RKQLATKA...SAPSTG.VKKPH.Y.P..VAL..IRRYQKSTELLI.KLPFQ.
Retrocopy MAPAKLTAGKSTGGKAARKQLATKAVCTSAPSTGRVKKPHCY*PESVALGKIRRYQKSTELLICKLPFQS

Parental  LVREIAQDFKT-DLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          L.R.IAQDF.T..L.FQSAAIGALQ...EAYLVGL.EDTNL.AI.AKRV..MPKD.QLAR.IR.ERA
Retrocopy LLRKIAQDFNT>NLHFQSAAIGALQDTNEAYLVGLSEDTNLRAIYAKRVPMMPKDSQLARCIRVERA

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_4243 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4243 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 10 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243 , retro_tbel_4350, retro_tbel_674,