RetrogeneDB ID: retro_tbel_3690

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148584:32042..32468(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E1B
• Ensembl ID: ENSTBEG00000001631
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 1B [Source:HGNC Symbol;Acc:33179]

Sequence

>retro_tbel_3690
CCTCTACAGAACAGATGGGCACTCTGGGCTTTTAAAAATAATGAAAGTAAAACTTGGCAGACAAACATTCAACTGATCTC
TAAGTTGGATACTGTTGAAGACTTTTGGGCTCTGTACTACCGTATCTAGTGGTCTGGTAACTTAATGCCTGTCTGTGACT
ATTCACCTTTTAAGAATGGTATTGAGCTTATGTGGGAAGATAAGAAAAATGAATGAGGAGAATGATGGCTAATGACATAG
AGCAAACAGCAGAGATGGAGTGACTTCTATTGCTTTTGGCTGGAGACACTGCTATACCTTATGGGAGAATCTTTTGATGA
CTACAGTGATGATGTGTGTGAAGCTGTTGTTAATGTTAGAACAAAAGGCTATAAGACAGCAATGTGGACTACTAAATGAG
AAAATAGAAAAGTTGTCACATATATA

Alignment

ORF - retro_tbel_3690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.52 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPTRWALWFFKNDRSRAWQDNLHLVTKVDTVEDFWALHQHIQLASKLSPGCDYALFKDGIRPMWEDSRN
          P...RWALW.FKN..S..WQ.N..L..K.DTVEDFWAL...I.....L.P.CDY..FK.GI..MWED..N
Retrocopy PLQNRWALWAFKNNESKTWQTNIQLISKLDTVEDFWALYYRI*WSGNLMPVCDYSPFKNGIELMWEDKKN

Parental  KRGGRWLVSLAKQRRHSELDRLWLETLLCLIGESFAEHSREVCGAVINVRAKGDKLAVWTMEAENQAGVL
          ..G..WL....KQ.R.S.....WLETLL.L.GESF...S..VC.AV.NVR.KG.K.A.WT...EN...V.
Retrocopy E*GE*WLMT*SKQQRWSDFYCFWLETLLYLMGESFDDYSDDVCEAVVNVRTKGYKTAMWTTK*ENRKVVT

Parental  YI
          YI
Retrocopy YI

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_3690 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3690 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088, retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690 ,
Tupaia belangeri	ENSTBEG00000004455	11 retrocopies	retro_tbel_1299, retro_tbel_2197, retro_tbel_2623, retro_tbel_2680, retro_tbel_3932, retro_tbel_4471, retro_tbel_4622, retro_tbel_536, retro_tbel_616, retro_tbel_650, retro_tbel_714,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,