RetrogeneDB ID: retro_tbel_153

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1326:7917..8223(-)
• Located in intron of: ENSTBEG00000001732

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL1
• Ensembl ID: ENSTBEG00000016751
• Aliases: None
• Description: cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]

Sequence

>retro_tbel_153
GATAAAGACTGCGCTATGTCGCTATGATGTGACCTGTGAGACCAAAGAGAGCAAAGGGGAAGACCTGTGTCATCTCTGGG
CCCCCGAATGTGCTCCCCTAAGAGCAGAATGATCTATGCCAGCTCCAGGGATACCATCAAGAAGAAACTGACAGGGATCA
AGCATGAATTACAGGCAAACTGCCAAGAGGAGGTCAAGGACCACCACAACCTGGCAGAGAAGCTGGGAGGCAATGCTGTC
ATCTCCCTGGAGGGCAAACCTTTGTGTGCCCCCTCCAGTCCCCTGCCTGGAGCATCTGGCAGCCCC

Alignment

ORF - retro_tbel_153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKDC-RYAL-YDATYETKESKKEDLVFIFWAPECAPL-KSKMIYASSKDAIKKKLTGIKHELQANCYEEV
          DKDC.RY...YD.T.ETKESK.EDL....WAPECAPL.KS.MIYASS.D.IKKKLTGIKHELQANC.EEV
Retrocopy DKDC<RYVA<YDVTCETKESKGEDLCHL-WAPECAPL<KSRMIYASSRDTIKKKLTGIKHELQANCQEEV

Parental  KDRCTLAEKLGGSAVISLEGKPL-APSTRLPGASGSP
          KD...LAEKLGG.AVISLEGKPL.APS..LPGASGSP
Retrocopy KDHHNLAEKLGGNAVISLEGKPLCAPSSPLPGASGSP

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_153 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_153 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 12 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus	ENSCJAG00000001916	1 retrocopy	retro_cjac_347,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Myotis lucifugus	ENSMLUG00000024685	6 retrocopies	retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127, retro_mmus_3556, retro_mmus_719, retro_mmus_970,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii	ENSOGAG00000016503	8 retrocopies	retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Tupaia belangeri	ENSTBEG00000016751	2 retrocopies	retro_tbel_153 , retro_tbel_3085,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,