RetrogeneDB ID: retro_tbel_2680

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_116196:46407..47098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSTBEG00000004455
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_tbel_2680
AACAAGTTCAACGCCTTGAAAGATGATGACAATGGGGCCCATGATCAGAATGAAGAAAATAGCACACAGAAAGGTGGTGA
GAAGGAAAAATTGGACTGGGGCAAGAATCAGAGCAGTAGCAAGAGGAAAGCTGTCACCCCTGGACCAACAGAGCATCCCC
TGCATGTACAATTACGCTCTGGGACTCTAGGAGGACCCCCAGCCACCCCGCAAGTTCACAGAGCTATGAACAAAGCAGGT
CAACCCTTCACAGCGGAGCAGTTCCGGAGGTTTTATAGCCACATGTCATGTCCTGGGGACCTGACAGACCACAGTGACTT
TCATCTCTTCAAAGAAGGAGTTAAACCCATGTGAGAGGAAGATGCAAATAAAAATGGTGGCAAGTGGATTATCTGCCTGT
GGAAGGGCTTGGCCTCCCATTTGCTGGGAGAACCATCCTGGCTGTCTCGGGGGAACAGTTCATGGTGGAGGAGAGGATCT
GTAGGGCTGTGATCTCTGTCCGCTTTCAGGAGGACATACTTTTAATCTGGAATCAGACTGCCCGCAACCAAGCTACACAG
CCCGAATCCAGAATAGGCTTCGGCAAGGGCCTAACCTACCTCCCAACACCATTATGGAATACAAAACTCATGCTGACAGC
ATCAACATGCCAGGCAGGCTGGGCCTCCACAGGCTCCTTCTTCAAAACCTC

Alignment

ORF - retro_tbel_2680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.81 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKFDALKDDDSGDHDQNEENSTQKDGEKEKAERDKSQGSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRP
          NKF.ALKDDD.G.HDQNEENSTQK.GE..K...D.....S..K.....P...P............T.G.P
Retrocopy NKFNALKDDDNGAHDQNEENSTQKGGE--KEKLDWGKNQSSSKRKAVTPG--PTEHPLHVQLRSGTLGGP

Parental  TSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRK-
          .............G.....EQF.RFYSHM..PGDLT.HSDFHLFKEG.KPM.E.DANKNGGKWII.L.K.
Retrocopy PATPQVHRAMNKAGQPFTAEQFRRFYSHMSCPGDLTDHSDFHLFKEGVKPM*EEDANKNGGKWIICLWK<

Parental  GLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQAT-TARIRDTLRRVLNLPPNT
          GL........ILA..GEQFMV.E.IC.AV.SVRFQEDI..IWN.TA..QAT.TARI...LR...NLPPNT
Retrocopy GLGLPFAGRTILAVSGEQFMVEERICRAVISVRFQEDILLIWNQTARNQAT<TARIQNRLRQGPNLPPNT

Parental  IMEYKTHTDSIKMPGRLGPQRLFSKPL
          IMEYKTH.DSI.MPGRLG..RL....L
Retrocopy IMEYKTHADSINMPGRLGLHRLLLQNL

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_2680 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2680 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
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
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,