RetrogeneDB ID: retro_tbel_2508

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_112333:15277..15968(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSTBEG00000009970
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_tbel_2508
CTTAAGATTGACAGTGATGTTCAAGAACCAGCAGAACCAGAGGATGACCTTGACATTATGCTTAGCAATAAAAAGAAGAA
AAAGAAGAATGCTAAGTTCCCAGATGAGGATGAAATGCTAGAGAAAGACGAAGCTTTAGAAGATGAAGACAGCAAAAAAG
ATGGTGGTATCTCATTCAGGAGCCAGGCAGGTCCAGCTTGGGCCAGCTCAGAAAGAGGTCACACATGACGAGCTACTGAC
TCCAGTGCTTAACATTGTGAGGGAAAAGAATCTGGCTACGTTGCTGGAGAGAAAAGGACATTTGTCAGGAAACCTCCGCA
ACTTGTCCGAGCAGAAACTAAGACACCTTCTTCTGGCAACTTTACGTATCTCTGTAAACTACTCCATGGTCGACCCAGAC
ACCTTGCGTTTTATTGGCTGGATTGGGTATAAGTGGTTCTACAAATGGTAATAACCAACTAGTAATCAAAGGAAGATCCA
ACAGAAACAGACAGAAACTGTCTTGAGAAGGTATACCAAGGAATATGTCCCTTGTCACACAGGCCGATCACTGGACACGA
TCTTGCAGAAGGATACTTGACTCTATTTCTTACAGGGCGAAACTTGTCATTCTCGATGCTCTGTTGCCAGTATCAAAACC
GGCTTCCAGGCTGTCACAGACGAGTGAGCACACCTCCACACCACAGCTAAC

Alignment

ORF - retro_tbel_2508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 70.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKIDSDVQEPAEPEDDLDIMLGNKKKKKKNVKFPDEDEILEKDEALEDEDSKKDDG-ISFSNQTGPAWAG
          LKIDSDVQEPAEPEDDLDIML.N........KFPDEDE.LEKDEALEDEDSKK.DG..S.S.........
Retrocopy LKIDSDVQEPAEPEDDLDIMLSNXXXXXXXAKFPDEDEMLEKDEALEDEDSKK-DG>VSHSGARQVQLGP

Parental  SERDYTYEELLNRVFNIMREKN-PDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICKLLHRQPKHLLA
          .....T..ELL..V.NI.REKN....VAGEKR.FV.KPPQ.VR..TK..S..NFT..CKLLH..P.HL.A
Retrocopy AQKEVTHDELLTPVLNIVREKN<SGYVAGEKRTFVRKPPQLVRAETKTPSSGNFTYLCKLLHGRPRHL-A

Parental  F-LLAELGTSGSIDGNNQLVIKGR-FQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLYFLQCETCH
          F.LLA.LG.SGS..GNNQLVIKGR..QQKQ.E.VLRRY.KEYV.CHT.RS.DTILQKDT.LYFLQ.ETCH
Retrocopy F<LLAGLGISGSTNGNNQLVIKGR<IQQKQTETVLRRYTKEYVPCHTGRSLDTILQKDT*LYFLQGETCH

Parental  SRCSVASIKTGFQAVTGKRAQLRAKAN
          SRCSVASIKTGFQAVT...A.L...AN
Retrocopy SRCSVASIKTGFQAVTDE*AHLHTTAN

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_2508 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2508 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508 ,