RetrogeneDB ID: retro_tbel_1911

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5983:854452..854706(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD4
• Ensembl ID: ENSTBEG00000016033
• Aliases: None
• Description: FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Sequence

>retro_tbel_1911
ATGGAAAGAGTGACCAGGGCCCTTCTGCTGACAAGCCTAACTGCCCTAGAAGCCAATGACCTGTTTGATAAAGACAGCCC
CTTCTACTATGACTGGGAGAGCCCACAGCTGGCCGGGTTATCTGTGGAGGGATTCTGGGCGTCGCTGGGCTCTAGTTGGC
CCTGAGCGGCAAGTTGAAGTGCAGGCGTGACCAGATGCACAGCCCCTGGTCTGAGAAAGCCACCCCACTCATTGCTCCAG
GCACTGCCGGCTCC

Alignment

ORF - retro_tbel_1911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MERVTRALLLLAGLPALKANDLFADKDSTFYYDWESLQLAGM-ICAGILGITGIAIALSGKCKCRHDQVH
          MERVTRALLL...L.AL.ANDLF.DKDS.FYYDWES.QLAG..IC.GILG..G...ALSGK.KCR.DQ.H
Retrocopy MERVTRALLLTS-LTALEANDLF-DKDSPFYYDWESPQLAGL<ICGGILGVAGL*LALSGKLKCRRDQMH

Parental  SPLAEKATPFIAPGSASS
          SP..EKATP.IAPG.A.S
Retrocopy SPWSEKATPLIAPGTAGS

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_1911 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1911 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148, retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911 ,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70, retro_tsyr_875,