RetrogeneDB ID: retro_itri_545

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:1737958..1738701(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSSTOG00000008976
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_itri_545
AGAAATGACATAGATAATTATTCTGTGAGTTCTCCACTCCAGTCTCTTCAGCAGTGACCATGGCTCATTTATGGTCTCTT
GTTTTCTTCAACCACTCCAAAGATTGTGATAATATGATTGATTTCTTCCTTTACCAGCCACAGTATCTTAAGGCAGCTCA
GGCAGTGTGTTCACATATTTTCTGCCACATGACTCCTGTGGTCATAATGAACAAAGATGTTTGACAATGATGAAAATGCT
AAAGAATCTAGTAAAAGTTATGCAGTCAGAGTCTCACACATCCAAAGACCCAATTACAGAATTTGTTGAATGCCTGTATG
TTAACTTTGACTTTAATAGGGCTCAGAAGATGCTGAGGGGATGTGCATCAGTGCTGTGGATGACTTGGTGGCTTGTCACG
AGAATTTCATTGAAAATGCCCCATCTCTTCCATATTTGAGACTTTTGGTTATATCCACCAGTGTATCAGTATTAATATGT
TGGTAGATTAAACTGAACATAACTCCAGAAGAGGCTGAGAAGTGGATTGTGAATTTGATTAGAAATGAAAGACTGGATCC
CAGATTTATTCTAAATGAGGTTGTGTGATTATGAGTAACAGTGCAGTCTCACCTTATCGGCAAGTAATTGAAAAGACCCA
AAGCCTTTCTTTTAGAAGCCATATGTTGGTCATGAATATTGAAAAGAAACTTATTCAGAATAGTAGGTAAGAGGCTCCTA
ACTGGACAACCGTAGATTCTGGG

Alignment

ORF - retro_itri_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.54 %
• Parental protein coverage: 96.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KETIDNNSVSSPLQSLQQRTWLIH-WSLFVFFNHPKGRDNIIDLFLYQPQYLNAIQTMCPHILRYLTTAV
          ...IDN.SVSSPLQSLQQ..WLI..WSL.VFFNH.K..DN.ID.FLYQPQYL.A.Q..C.HI....T..V
Retrocopy RNDIDNYSVSSPLQSLQQ*PWLIY<WSL-VFFNHSKDCDNMIDFFLYQPQYLKAAQAVCSHIFCHMTPVV

Parental  ITNKDVRK-RRQVLKDLVKVIQQESYTYKDPITEFVECLYVNFDFDGAQKKLRECESVL-VNDFFLVACL
          I.NKDV.......LK.LVKV.Q.ES.T.KDPITEFVECLYVNFDF..AQK.LR.C.SVL.V.D..LVAC.
Retrocopy IMNKDV*Q<MMKMLKNLVKVMQSESHTSKDPITEFVECLYVNFDFNRAQKMLRGCASVL<VDD--LVACH

Parental  EDFIENA-RLF-IFETFCRIHQCISINMLAD-KLNMTPEEAERWIVNLIRNARLD-AKIDSKLGHVVMGN
          E.FIENA..LF.IFETF..IHQCISINML.D.KLN.TPEEAE.WIVNLIRN.RLD...I.SK.G.V.M.N
Retrocopy ENFIENA>HLF>IFETFGYIHQCISINMLVD>KLNITPEEAEKWIVNLIRNERLD<SQIYSK*GCVIMSN

Parental  NAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSEAPNWATQDSG
          .AVSPY.QVIEKT.SLSFRS.ML.MNIEKKL.QNSR.EAPNW.T.DSG
Retrocopy SAVSPYRQVIEKTQSLSFRSHMLVMNIEKKLIQNSR*EAPNWTTVDSG

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_545 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_545 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545 ,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,