RetrogeneDB ID: retro_itri_1425

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393482.1:1777297..1777615(-)
• Located in intron of: ENSSTOG00000022898

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSSTOG00000012552
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_itri_1425
AAAAAATTTTACAAAGAAACAGAAGGCAGCGTTGCTGGAGTACATGAAAAAATGCTGAGCAGAAAAAGCAGATTCTTCAA
GCCAAACAAATACAAAAAAATTGCTCAGAGCATGATGCTTTGGCAAAAATGATCCAGCATCATCCAAACAGGCACAAGAC
ACTAAAGGAACCAGAGGCTCTGAGGAAAGAATTAGAGCACACCTTTCACAGACTAAAGAAAGCACTGAAGATAAGCTGGA
ATTGAGACAGAAACAGCATCACATTCTTCTCATACCATCTACACCATTCAGCAAACATTGGAAAATGACAAAAAGCTC

Alignment

ORF - retro_itri_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 53.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKIYKEIECSIAGAHEKI-AECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELEALGKELEHLS
          .K.YKE.E.S.AG.HEK..AE.KKQILQAK.I.KN..E.DALAK.IQHHP.RH.TLKE.EAL.KELEH..
Retrocopy KKFYKETEGSVAGVHEKM<AEQKKQILQAKQIQKNCSEHDALAKMIQHHPNRHKTLKEPEALRKELEHTF

Parental  H-IKE-SVEDKLELRRKQFHVLL-STIHELQQTLENDEKL
          H..K..S.EDKLELR.KQ.H.LL..TI...QQTLEND.KL
Retrocopy HRLKK<STEDKLELRQKQHHILL<HTIYTIQQTLENDKKL

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_1425 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1425 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031, retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425 ,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,