RetrogeneDB ID: retro_tbel_4388

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_80198:4548..4816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LITAF
• Ensembl ID: ENSTBEG00000017097
• Aliases: None
• Description: lipopolysaccharide-induced TNF factor [Source:HGNC Symbol;Acc:16841]

Sequence

>retro_tbel_4388
GCTGTGAATACCATCTATGTGTAGCAGCCCATCTCCTTTTTTGACCTCCCTGCCCAAACCTGTTGTCCCTCCTGCAACAA
GATGATCAGGATTTAACTGTCCTACAATGATGGTGTTCTCACCTAGCTTTATTGAGGGAACCTGTGCCTGCTGGTGTGTA
TAGCTGGCTGCCACTTCTCCTTCTGTTCCAATGTTCTGCAGAATGTAGAGCACTACTGTCTCCACTGCAGAGGTCTCCTG
GGCACTAAAAATCTTTGTAGGACTGGTT

Alignment

ORF - retro_tbel_4388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVQTVYVQQPVSFFDRPVQMCCPSCSKMIVTQLSYNAGALTWLSCGSLCLL-GVYSWLPLLLLFQCSAEC
          AV.T.YV.QP.SFFD.P.Q.CCPSC.KMI...LSYN.G.LT.L..G.LCLL.GVYSWLPLLLLFQCSAEC
Retrocopy AVNTIYV*QPISFFDLPAQTCCPSCNKMIRI*LSYNDGVLT*LY*GNLCLL<GVYSWLPLLLLFQCSAEC

Parental  RALLSPLQRSPGH-LKIFVGLV
          RALLSPLQRSPGH.LKIFVGLV
Retrocopy RALLSPLQRSPGH<LKIFVGLV

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_4388 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4388 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388 ,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,