RetrogeneDB ID: retro_itri_1173

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393393.1:2783500..2784013(+)
• Located in intron of: ENSSTOG00000008672

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP1
• Ensembl ID: ENSSTOG00000008178
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:HGNC Symbol;Acc:10648]

Sequence

>retro_itri_1173
CAATCATTAGAAGAAAGTGCTCACTCTAAGCCTATAGATGTTTCCTATCTGGATCCTCAAATTGGTTGCATTATTACTGC
CAAAAAACACCTGATACAGATTTTTGCATGTAGAAAAAGTAGATGTTGGAGAAATAGCCCCCAGAACAGTTGTCAGTGCC
CTGGTGAATCATGTTCCCTTTGAAAAGATGCAGAATCAAATGATTTCACTTTATAAACTGAGACCTGCCGAGATGAGGGG
TGTACCATCTCAAATAATGGGAATGTGTGATGTTTCACCAGAAGTGGATAGTTTGGCTCCTCTTAGCAGGTCTCTTCCTG
GAGACTGAATGACTTTTGATACTTTCCCTGGAGAGACTGACAAGGACCTGAATCCTAAGTAGATGATTGGAGATCAGATC
AAACCTGACCTGCACACTAATTAGTAGCATGTGGCTACAAAAAAGGAGTTCCCTCTGAGGAGAAAGGGAAGGGAGCAAAC
AGGGCTCAATTTATGACCAACAGTGAAATCAAA

Alignment

ORF - retro_itri_1173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.97 %
• Parental protein coverage: 53.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QSLAGSVDSKPIDVSRLDLRIGCIITAKKH-PDADS-LYVEEVDVGETVPRTVVSGLVNHVPLEQMQNRM
          QSL..S..SKPIDVS.LD..IGCIITAKKH.PD.D..L.VE.VDVGE..PRTVVS.LVNHVP.E.MQN.M
Retrocopy QSLEESAHSKPIDVSYLDPQIGCIITAKKH<PDTDF<LHVEKVDVGEIAPRTVVSALVNHVPFEKMQNQM

Parental  VILLCNLKPAKMRGVLSQAMVMCASSPEKVEILDPPNGSVPGDRITFDTFPGEPDKELNPKKKIWEQIQP
          ..L...L.PA.MRGV.SQ.M.MC..SPE.V..L.P...S.PGD..TFDTFPGE.DK.LNPK..I..QI.P
Retrocopy ISLY-KLRPAEMRGVPSQIMGMCDVSPE-VDSLAPLSRSLPGD*MTFDTFPGETDKDLNPK*MIGDQIKP

Parental  DLYTNDEGVAT-YKGAPFEVKGKGVCRAQTMTKSGIK
          DL.TN...VAT..KG.P.E.KGKG..RAQ.MT.S.IK
Retrocopy DLHTN**HVAT<KKGVPSEEKGKGANRAQFMTNSEIK

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_1173 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1173 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173 ,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,