RetrogeneDB ID: retro_itri_1455

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:2069319..2069997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSSTOG00000021318
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_itri_1455
GACTTATTTCTTGAAGTCCAGATTCAGAATATGTCATCTTCAACTGTGTTTATACAAAAGGTTTCCTTAGAGCCATCTGA
AATGTACACTGGAGTAGAATTAAATACTGTTAACCAGGGAGGAGAAGATGAGTGTACCTTTGGAACAAGGACATTTTTGC
AATCAACAGAAGGACGCCAGTACTTATACCACCTTCAGCTGAAACCAGAATATTCAGAGAAAGCTAGTACTATTAGGGGA
CTAATGGAAATGGGAAAATTAGATATATTATGGAAAAGAAACCTGGGTGAAATGGCAATACTACAGACAATCCAGCTTGA
AAGAGAGGCTCCATTTTATGGAAACATAAAGCTGTCTTTAGAGAAAATCCCAGATACTGTAATTATGGAAGAGCCTTTTC
ATATTACCTGCAAGATAACAAACTGTAGTGATAAGAAAATGAAATTGGTTTTGAAAATGTGTGATACACCTTCTGTTCGT
TGGTGTGGAAATTCAGGAAGGTATCTTGGAAAGCTGCCCACAAAGTCATCTCTCTGCTTTACCCTAACACTACTGTCCTT
AAAATTGGGCCTGCAAAGTATTTCTGGCATACGAATAACAGACAAAGTATTAAGGAAAACATATGACTATGATGATGTTG
CAAATGTCTTTGTAGTACCTTCCATCGTTAAAATGAAA

Alignment

ORF - retro_itri_1455 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.23 %
• Parental protein coverage: 63.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVFLEAQIQNITTSPMFMEKVSLEPSIMYNVTELNSVNQAGECLSTFGSRAYLQPMDTRQYLYCLKPKKE
          ..FLE.QIQN...S..F..KVSLEPS.MY...ELN.VNQ.GE...TFG.R..LQ....RQYLY.L..K.E
Retrocopy DLFLEVQIQNMSSSTVFIQKVSLEPSEMYTGVELNTVNQGGEDECTFGTRTFLQSTEGRQYLYHLQLKPE

Parental  FAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKIT
          ..EKA..I.G....GKLDI.WK.NLGE...LQT.QL.R.AP.YG...LSLE.IPDTV..EEPFHITCKIT
Retrocopy YSEKASTIRGLMEMGKLDILWKRNLGEMAILQTIQLEREAPFYGNIKLSLEKIPDTVIMEEPFHITCKIT

Parental  NCSSERTMDLVLEMCNTSSIHWCGISGRQLGKLHPSSSLCLALTLLSSVQGLQSVSGLRITDTFLKRTYE
          NCS....M.LVL.MC.T.S..WCG.SGR.LGKL...SSLC..LTLLS...GLQS.SG.RITD..L..TY.
Retrocopy NCS-DKKMKLVLKMCDTPSVRWCGNSGRYLGKLPTKSSLCFTLTLLSLKLGLQSISGIRITDKVLRKTYD

Parental  YDDIAQVCVVSSAVKVE
          YDD.A.V.VV.S.VK..
Retrocopy YDDVANVFVVPSIVKMK

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_1455 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1455 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455 ,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,