RetrogeneDB ID: retro_tbel_616

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2555:62528..63250(-)
• 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_616
CATGATCAGAATGAAGAAAACAGCACACAGAAAGATGGTGAGAAGGAAAAAGCAGACTGGGACAAGAGTCAGGGCAGCAG
CAAGAGGAAGGCTGTCATCCCTGGACCAGCAGAGCATCCCCTGCAGTACAACTACACTTTCTGGTACTCCAGGAGGACCC
CCAGCCATCCCACGAGTTCACAGAGCTATGAACAGAATATTAAACAGATTATCACCTTCGCCTCTGTGGAGCAGTTCTGG
AGGTTTTATAGCCACATGGTTTGTCCTGGGGACCTGACAGGCCACAGTGACTTCCATCTCTTCAAAGAAGGAATTAAACC
CATGTGGGAGGATGATGCAAATAAAAATGGTGGCAAGTGGATTATTCAGCTGTGGAAGGGCTTGGCCTCCCCTTGCTGGG
AGAATCTCATCCTGGCCATGTTGGGGGAACAGTTCATGGTTGGGGAAGAGATCTGTGGGGCTGTGGTCTTTGTCCGCTTT
CAGGAGGACATCATTTACATCTGGAATAAGACTGCCAGTGACCAAGCTACCACAGCCCGAATCCGGGATACACTGCAGCA
AGTGCTTAACCTACCTCCCAACACCATTATGGAATATAAAACTCACACCGACAGCATCAAAATGCCAGGCAGGCTGGGCC
CCCAAAGGCTCCTTTTTCAAAACCTCTGGAAGCTGCAGTTGAATGTGCCATGACCCTCTTCCTCTCTGGATGGCACCGTC
AT

Alignment

ORF - retro_tbel_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HDQNEENSTQKDGEKEKAERDKSQGSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQI
          HDQNEENSTQKDGEKEKA..DKSQGSSKRKAV.PGPAEHPLQYNYTFWYSRRTP..PTSSQSYEQNIKQI
Retrocopy HDQNEENSTQKDGEKEKADWDKSQGSSKRKAVIPGPAEHPLQYNYTFWYSRRTPSHPTSSQSYEQNIKQI

Parental  GTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAM
          .TFASVEQFWRFYSHMV.PGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWII.L.KGLAS.CWENLILAM
Retrocopy ITFASVEQFWRFYSHMVCPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIQLWKGLASPCWENLILAM

Parental  LGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTHTDSIKMPG
          LGEQFMVGEEICGAVV.VRFQEDII.IWNKTASDQATTARIRDTL..VLNLPPNTIMEYKTHTDSIKMPG
Retrocopy LGEQFMVGEEICGAVVFVRFQEDIIYIWNKTASDQATTARIRDTLQQVLNLPPNTIMEYKTHTDSIKMPG

Parental  RL-GPQRL-FSKPLEAAVECAMTLFLSGWHRH
          RL.GP....FSKPLEAAVECAMTLFLSGWHRH
Retrocopy RL<GPPKAPFSKPLEAAVECAMTLFLSGWHRH

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_616 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_616 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,