RetrogeneDB ID: retro_itri_279

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:36604684..36605133(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA7
• Ensembl ID: ENSSTOG00000012489
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 7 [Source:HGNC Symbol;Acc:9536]

Sequence

>retro_itri_279
CAGCTTAAAAGAACTGTGAGGAAAATTTGTGTGCTTGATGATCACATCTGCATGGCTTTTGGAGGACTGACTGCTGATGG
TAGAGTTGTAATAAACAGAGCCGGGTTGAGTGCCAGAGCCATAAGCTTACAATTGAGGACCCTGTCACTGTAGAATAATA
TGTAACTCGATTCATAGCACCTTTAAAGCAGAAATATACTCAGACCAATAGAAAAAAGCCTTTTAATATCTCTGCCTTAA
TTGTAGGTTTTGATAATGATGGTATCCTAAGATTATATCAGACAGATCCCTCTGGTACTTACAATGCATAGAAAGTAAAT
GCAATAGGCCCAAGTGCTAAAACAGTCCCAGAATTTCTAGAAAAGAATCACACAGAAGATGCGATAGGAAATGACAATGA
AGTTATCAAATTAGCAATAAGAGTTTTGCTAAAAGTTGTCCAGTCTGGT

Alignment

ORF - retro_itri_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 68.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QDERTVRKICALDDNVCMAFAGLTADARIVINRA-RVECQSHRLTVEDPVTVE-YITRYIASLKQRYTQS
          Q..RTVRKIC.LDD..CMAF.GLTAD.R.VINRA.RVECQSH.LT.EDPVTVE.Y.TR.IA.LKQ.YTQ.
Retrocopy QLKRTVRKICVLDDHICMAFGGLTADGRVVINRA<RVECQSHKLTIEDPVTVE*YVTRFIAPLKQKYTQT

Parental  NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLV
          N...PF.ISALIVGFD.DG..RLYQTDPSGTY.A.K.NAIG..AK.V.EFLEKN.T..AI..D...IKL.
Retrocopy NRKKPFNISALIVGFDNDGILRLYQTDPSGTYNA*KVNAIGPSAKTVPEFLEKNHTEDAIGNDNEVIKLA

Parental  IKALLEVVQSG
          I..LL.VVQSG
Retrocopy IRVLLKVVQSG

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_279 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_279 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279 ,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,