RetrogeneDB ID: retro_itri_1268

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393420.1:1816816..1817228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSSTOG00000005615
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_itri_1268
AGGTTGATGCAGAAAGTTTATAAGACCTACAATGAAATCAAACCCTGATGCTGCTAGCACGGCTATTGATTATGTACAGA
GACAGCTGTGCTATTGTGGAATTCATAACTACTTAGACTGAGAGAATACAGGTTGGTTCAAACAAACCTAAAACTAGACT
ATCCCTGTTAATTGCTCCAGAGAGTCTGCTATTAGATGTAATGACAGCCTGGCCAATCTCTCTCACCTTTATCCTGAGGG
GTGTGAGGCTCTAGTTGTGAAGAAGCTACAAGAAATCCTGATGCATGTTTTCTGGGCAGTGCAGGCCTTTATAGCTGTGC
AGATGCTGGGCATGCAGGGTGCATGCATCATGTTGTGAAGAGGGAGTAGAGATCTTGCTTATAAGCTCCTCATCACTGGC
AGAACTTATGCA

Alignment

ORF - retro_itri_1268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.29 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRIQKVYKTYNG-TNPDAASRAIDYVQRQLQCCGIHNYSDWENTDWFKETKNQSVPLSCCRETASSCNGS
          R..QKVYKTYN...NPDAAS.AIDYVQRQL..CGIHNY.D.ENT.WFK.T.N...P..C.RE.A..CN.S
Retrocopy RLMQKVYKTYNE>SNPDAASTAIDYVQRQLCYCGIHNYLD*ENTGWFKQT*N*TIPVNCSRESAIRCNDS

Parental  LANPSDLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGMLCACIVLCRRSRDPAYELLITGGTYA
          LAN.S.LY.EGCEALVVKKLQEI.MHV.WA..AF.A.Q.LGM..ACI.L.R.SRD.AY.LLITG.TYA
Retrocopy LANLSHLYPEGCEALVVKKLQEILMHVFWAVQAFIAVQMLGMQGACIML*RGSRDLAYKLLITGRTYA

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_1268 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1268 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268 ,