RetrogeneDB ID: retro_itri_1815

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393887.1:159611..160172(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004124
• Aliases: None
• Description: None

Sequence

>retro_itri_1815
GGTGGAGAGTACAGTGAAGACAACGTTAATGAATTAGGGAAGGAAGCTGAAGTGGACAGTGTACAGCAGACAAAGAAACC
CACAGGTGAAAAAATAAGGCTCTGAATATTCCAGCCAGGAAGAGAAAACAAAAGTGGGCCATTGGTACAAGAGGAAGAGG
AGTATGTCAAGGCAGGATGTGGAAGACATAGCAGTGAGGAAGAAGATGGACCAGGAGCAGGAAAGAGGTATTGAGTCAGG
GATACATGGAAATAGAATGAGGAGGAACTCTAGGCGAGCTTATAAAGTGTGTGAAACCAAAAACCAAAAGCCCTTGACTA
TACAATTTAAACAGGAGAGGAGATTGAAGAGACAAGTTCAGGTGAACTCTTGGTCAAAGCAGAAGAGCTACAGAGACCTA
AATAAAACGAGGGAGTTAAAATCACCAACATGTCGGTTTTGCTGGTAAAGAAGTGAGGGTGAGTGAGAAGTGGATGCTAC
ATCTAAAGTTAAATCCGTCTTCAAGCAATGAGAAAGAAAAAAACACAGGTTAACATCCCTTCAGCAGGCTACTCACTTCC
T

Alignment

ORF - retro_itri_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.21 %
• Parental protein coverage: 97.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  GGEYSEDDVNELVKEDEVDGEEQAQKPKGKQ-RKAQSIPARKRKQ-SGLLLEEEEEDAKAESGGSSSEEE
          GGEYSED.VNEL.KE.EVD...Q..KP.G....KA..IPARKRKQ.SG.L..EEEE..KA..G..SSE.E
Retrocopy GGEYSEDNVNELGKEAEVDSVQQTKKPTGEK<NKALNIPARKRKQ>SGPLVQEEEEYVKAGCGRHSSE-E

Parental  DE-TEEQEKGTGS-EDARKKKEDELWASF-LNDVGPKSKL-PSSTQVK-TGEETEEMSSSKLLVKAEELE
          .....EQE.G..S..D..K..E.EL.AS.....V.PK.K..P...Q.K.TGEE.EE.SS..LLVKAEEL.
Retrocopy ED>DQEQERGIES<RDTWK*NEEEL*ASL<IKCVKPKTKS<PLTIQFK<TGEEIEETSSGELLVKAEELQ

Parental  KPKETEKVKITKV-FDFAGEEVRVTK-EVDATSKEAKSFFKQNE-KEKPQANVPSAVPSIP
          .PK..E.VKIT.....FAG.EVRV...EVDATSK..KS.FKQ.E.K.K.Q.N.PSA..S.P
Retrocopy RPK*NEGVKITNM<VGFAGKEVRVSE<EVDATSK-VKSVFKQ*E<KKKTQVNIPSAGYSLP

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_1815 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1815 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815 ,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,