RetrogeneDB ID: retro_itri_669

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:12244049..12244931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPTOR
• Ensembl ID: ENSSTOG00000013845
• Aliases: None
• Description: DEP domain containing MTOR-interacting protein [Source:HGNC Symbol;Acc:22953]

Sequence

>retro_itri_669
TTCAGAACACAAAGGGGCACCTTCCCTCTGGACAATGAAATAAGGAAGGCTTTTAAGAGAGGACACAGGCTGTATGAGAA
GTTGAGGAGCACTGAAAAACACACTCTTACAACCTAGGGAAGAGGAAGGGGTCAAGTATGAATGCACCTTCATGGCATTT
TAATTCCTGGATTGGCTGGTTCAGGAAGGTGAGACCACCACAAGAAAAGAGGCTGAGCAGCTTTGCCACCTTTGCCACCA
GCTAGTGGAGCATGGCATGATACAACATGTGTCCAACAAGCACCTGTTTGTGGACAGCAATCTTCTTTACCAGTTAAGAA
TGAACTTCAGTTGTAGAAGACTGATGGAGCTGCTCAAAGAAAAGTTCCCCTCCTGCCAAAAGAATCAAGACTGTCCCTTC
TGCCTGAGGAAGCAGAGCCATGACAATTGGAAATATACCAGCTTCATGCCACTTAGCCCAACAAGATCAAAATCCTGTCT
GCAGTACTGAGGAGCAGCATAAACAGTTGCTGAAGCAGTGACTATTTCAGTAGCAGCCCCACTCTCAGCAGCAGCCCTCT
TGCTCTGCAACCCGAAGTCTATGCTCAAGAGACCAGTCACTTCGGCACAACTCCTGATGCCTTGGGCAGGTTAAGCAAGG
AAGACGTTCACGACTGTTGGTGATGCAGTTGACTGGGGCTTTGTGGTACAAGGAAGTAAGCCATGCCATGTCCAGGAAGT
GGATCCCAGCAGCCCTACAGCCACAGCAGGAATGAAGATCTGTAAGTTCATCATCTTTGTAATGGGCTCAAAGTGCTGCA
CATAGACTGCTGGACCATGGACCATCTGATTCTTATATGCCCAAGGACAATAGTAATGAAAGTCATGAAGGAGTAATAGT
GC

Alignment

ORF - retro_itri_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.09 %
• Parental protein coverage: 71.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FRKDDGTFPLDNEV-KAFMRGQRLYEKLMAPE-NTLLQPREEEGVKYERTFMASEFLDWLVQEGEATTRK
          FR...GTFPLDNE..KAF.RG.RLYEKL...E.NTLLQPREEEGVKYE.TFMA..FLDWLVQEGE.TTRK
Retrocopy FRTQRGTFPLDNEIRKAFKRGHRLYEKLRSTE>NTLLQPREEEGVKYECTFMAF*FLDWLVQEGETTTRK

Parental  EAEQ---LCHRLMEHGIIQHVSNKHPFVDSNLLYQFRMNFRRRRRLMELLNEKSPSSQEAHDSPFCLRKQ
          EAEQ...LCH.L.EHG.IQHVSNKH.FVDSNLLYQ.RMNF..RR.LMELL.EK.PS.Q...D.PFCLRKQ
Retrocopy EAEQLCHLCHQLVEHGMIQHVSNKHLFVDSNLLYQLRMNFSCRR-LMELLKEKFPSCQKNQDCPFCLRKQ

Parental  SHDNRKSTSFMSVS-PSKEIKIVSAVRRSSMSSCGSSGYFSSSPTLSSSPPV-LCNPKSVLKRPVTSEEL
          SHDN.K.TSFM..S.P.K.IKI.SAV.RSS..SC.SS.YFSSSPTLS.S.P..LCNPKS.LKRPVTS..L
Retrocopy SHDNWKYTSFMPLS<PNK-IKILSAVLRSSINSC*SSDYFSSSPTLS-SSPL>LCNPKSMLKRPVTSAQL

Parental  LTPGAPYARKTFTIVGDAVGWGFVVRGSKPCHIQAVDPSGPAAAAGMKVCQFVVSV-NGLNVLHVDYRTV
          L.P.A..ARKTFT.VGDAV.WGFVV.GSKPCH.Q.VDPS.P.A.AGMK.C.F...V.NGL.VLH.D..T.
Retrocopy LMPWAG*ARKTFTTVGDAVDWGFVVQGSKPCHVQEVDPSSPTATAGMKICKFIIFV<NGLKVLHIDCWTM

Parental  SNLILTGPRTIVMEVMEELEC
          ..LIL..PRTIVM.VM.E..C
Retrocopy DHLILICPRTIVMKVMKE**C

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_669 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_669 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005497	1 retrocopy	retro_cjac_1898,
Dasypus novemcinctus	ENSDNOG00000015660	1 retrocopy	retro_dnov_747,
Ictidomys tridecemlineatus	ENSSTOG00000013845	1 retrocopy	retro_itri_669 ,