RetrogeneDB ID: retro_trub_6

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_52:1283257..1284493(+)
• Located in intron of: ENSTRUG00000010905

Retrocopy information

• Ensembl ID: ENSTRUG00000011113
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF4A2
• Ensembl ID: ENSTRUG00000005660
• Aliases: None
• Description: None

Sequence

>retro_trub_6
ATGGACGAATGCATCCCGAAAACAATGAGAGCAGACGTCTTCAGAAGTGGACGACCAGAGCGTCCAGAGCCGTGGCAGAT
GACGGAGAGGAAGCTGAGTTACAGCGTGGACAGTTTTGAGGGCATGATGCTGAACGAGAATCTTCTCAGAGGCATCTTTG
CGTATGGATTCGAGAAGCCTTCCGCCATCCAACAGCAGGCCATTGTTCCGTGCATCAAAGGCTTTGATGTCATCGCACAG
TCCCAGTCGGGCACTGGCAAGACGGCCACCTACGTCATTGCCGCCCTGCAGAGAATCGACATGATGAAAGAGGACACCCA
GGCTATTATTCTCGCACCCACCAGGGAGCTGGCCAACCAAATTCAGAAAGTGGTGCTCAGTCTGGGGGACTACATGGGGG
TCCGTTGCCATGCCTGCATTGGGGGGACGAGCATTCATGAGGACATGGAGAACCTGAGGTCAGCGAACCCTCACGTCATG
GTGGGAACACCAGGTCGCGTCTTTGACGTATTAGCACGCAGGGCCGTCTCTGCCAAGGCCATAAGACTGCTGGTGCTTGA
CGAAGCTGATCAGATGCTGGGTAATGGCTTCAAGGACCAGATTCATGAAATCTTCTGTAAGCTGCCCACCAATGTCCAAG
CCATCCTGCTGTCGGCGACCATGCCAGCTCATGTCCTGGAGGCCACAAAGATGTTCATGCAGGATCCAGTGAAAATTCTC
ATTAAAAGGGAGGAGCTGACCATGGAGGGCATTCAACAGTTCTACATTAAGACTGAAACAGAAGAGAAGAAGCTGGAAAG
CCTGTGTGGCCTGTACAGCACGCTCACCATAACTCAAGCTGTCATTTTTGTCAACACCAGAAAAAAGGCCGAATGGCTGA
CTCAGGAGCTGATGTCCAAGGATTTCACAGTCTCCGTTCTGCATAGTGAGATGGGGCAGAGCGAGAGGGATACCACCATG
AAGGAGTTCCGCTCCGGCTCCAGCCGAGTGTTCATCACCACCGACCTGCTGTCCCGAGGGATCGATGTTCAGCAAGTGTC
GCTGGTCATCAACTTTGACCTCCCGACCAAATTAGAGAGCTACATCCACAGGATCGGTCGCAGTGGCCGGTTTGGCAGGG
GGGGAGTGGCGATCAACATGGTGACGGAAGAGAGCCAACCCATGCTGGCCATTATTCAGAACTTCTATGACTTCAAAATC
AAGGAGCTTCCTGCAAACATGGTCGATATTGTCTGA

Alignment

ORF - retro_trub_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.8 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGPDGMEPDGIIESNWTEITDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTG
          G.P...EP....E.......D.F..M.L.E.LLRGI.AYGFEKPSAIQQ.AI.PCIKG.DVIAQ.QSGTG
Retrocopy GRPERPEPWQMTERKLSYSVDSFEGMMLNENLLRGIFAYGFEKPSAIQQQAIVPCIKGFDVIAQSQSGTG

Parental  KTATFAISILQQLEIDQKETQALVLAPTRELAQQIQKVILALGDYMGAACHACIGGTNLRNEIQKLQAEA
          KTAT..I..LQ........TQA..LAPTRELA.QIQKV.L.LGDYMG..CHACIGGT........L....
Retrocopy KTATYVIAALQRIDMMKEDTQAIILAPTRELANQIQKVVLSLGDYMGVRCHACIGGTSIHEDMENLRSAN

Parental  PHIVVGTPGRVFDMLTRGHLYSKLIKMFVLDEADEMLSRGFKDQIYEIFQKLSTNIQVVLLSATMPAEVL
          PH..VGTPGRVFD.L.R.....K.I...VLDEAD.ML..GFKDQI.EIF.KL.TN.Q..LLSATMPA.VL
Retrocopy PHVMVGTPGRVFDVLARRAVSAKAIRLLVLDEADQMLGNGFKDQIHEIFCKLPTNVQAILLSATMPAHVL

Parental  EVTKKFMRDPVRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFLNTRRKVDWLTEK
          E.TK.FM.DPV.IL.K.EELT.EGI.QFYI..E.EE.KL..LC.LY.TLTITQAVIF.NTR.K..WLT..
Retrocopy EATKMFMQDPVKILIKREELTMEGIQQFYIKTETEEKKLESLCGLYSTLTITQAVIFVNTRKKAEWLTQE

Parental  MHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIG
          ....DFTVS.LH..M.Q.ERD..M.EFRSGSSRV.ITTDLL.RGIDVQQVSLVIN.DLPT..E.YIHRIG
Retrocopy LMSKDFTVSVLHSEMGQSERDTTMKEFRSGSSRVFITTDLLSRGIDVQQVSLVINFDLPTKLESYIHRIG

Parental  RGGRFGRKGVAINFVTEDDRRVLRDIETFYNTTVEEMPMNVADLI
          R.GRFGR.GVAIN.VTE.....L..I..FY.....E.P.N..D..
Retrocopy RSGRFGRGGVAINMVTEESQPMLAIIQNFYDFKIKELPANMVDIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_6 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_6 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Canis familiaris	ENSCAFG00000013659	1 retrocopy	retro_cfam_378,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Dasypus novemcinctus	ENSDNOG00000011502	5 retrocopies	retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi	ENSETEG00000018565	3 retrocopies	retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Gorilla gorilla	ENSGGOG00000005867	2 retrocopies	retro_ggor_525, retro_ggor_712,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000007377	1 retrocopy	retro_mmur_525,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys	ENSNLEG00000006633	1 retrocopy	retro_nleu_2589,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii	ENSOGAG00000010729	2 retrocopies	retro_ogar_2830, retro_ogar_943,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus	ENSSTOG00000012601	1 retrocopy	retro_itri_858,
Tupaia belangeri	ENSTBEG00000002268	11 retrocopies	retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes	ENSTRUG00000005660	2 retrocopies	retro_trub_14, retro_trub_6 ,
Tarsius syrichta	ENSTSYG00000013050	3 retrocopies	retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,