RetrogeneDB ID: retro_tbel_1893

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5959:635393..636032(-)
• Located in intron of: ENSTBEG00000005362

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSTBEG00000012109
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_tbel_1893
GACAGTGATGTGCAGGGCAAAGAAGAAATCGACAGCCTTTCGAACAAAGTAGAAGAAAGAATGAAAGAATTGAATCAGGA
CAATACTGGGCGGATAAAAAGATTACCACCCATCGTTTGAGGAGGGGCCATTGACAGATACTGGCCCATCGCCAATGGGC
GCCTGGTCGAGTATGACATAGATGAAGTGGTATATGATGAAGATTCACCTTATCAGAACATTAAAATTTTACACTCGAAG
CAATTTGGAAATATTCTCATTCTGAGTGGGGATGTTAATTTGGCAGAGAGCGATTTGGCATATACCCGGGCCATCATGGG
CAGCGACAAAGAAGATTACACTGGCAAGGATGTACTGATTCTGGGAGGTGGAGATGGCGACATATTATGTGAAATAGTCA
AACTGAAACCAAAGATGGTCACTGTGGTAGAGATTGACCAAATGGTAATTGATGGGTGTAAGAAATACATGTGAAAAACG
TGTGGTGACGTCTTAGACAATCTTAAGGGAGACTGCTATCAGAAGGTTCTTATGGAAGACTGTATTCCAGTACTGAAGAG
GTACACCAAAGAAGGGAGAGAGTTTGATTATGTGATTAATGATTTGATGGCTGTTCCAATCTCCACCTCTCCAGAAGAA

Alignment

ORF - retro_tbel_1893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 68.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSDVQGKEEIDSLLNKVEERMKELNQDNTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSP
          DSDVQGKEEIDSL.NKVEERMKELNQDNTGR.KRLPPIV.GGAIDRYWP.A.GRLVEYDIDEVVYDEDSP
Retrocopy DSDVQGKEEIDSLSNKVEERMKELNQDNTGRIKRLPPIV*GGAIDRYWPIANGRLVEYDIDEVVYDEDSP

Parental  YQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMV
          YQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGS.KEDYTGKDVLILGGGDG.ILCEIVKLKPKMV
Retrocopy YQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSDKEDYTGKDVLILGGGDGDILCEIVKLKPKMV

Parental  TMVEXXXXXXXXXXXXXXKTCGDVLD-LKGDCYQ-VLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTS
          T.VE..............KTCGDVLD.LKGDCYQ.VL.EDCIPVLKRY.KEGREFDYVINDL.AVPISTS
Retrocopy TVVEIDQMVIDGCKKYM*KTCGDVLDNLKGDCYQKVLMEDCIPVLKRYTKEGREFDYVINDLMAVPISTS

Parental  PEE
          PEE
Retrocopy PEE

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_1893 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1893 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 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893 , retro_tbel_3570,