RetrogeneDB ID: retro_itri_447

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393292.1:1670875..1671248(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSSTOG00000004189
• Aliases: None
• Description: solute carrier family 25, member 39 [Source:HGNC Symbol;Acc:24279]

Sequence

>retro_itri_447
GTGATGACTGTTCCATCTATGACCATCTACTCACCACCTATGACCAATTCAAGGCTTCCTTTGTAGGCAAGCCCTAACTT
CTGACCTCTATGCACCAATCATTGCTGGCGCAGTAACTCACTTGGGCACTGTGAGAATGATCAGACCCCTGGAACTTGTG
CAGACAAAGCTGCAGGGCCAGCATGCATCAATACCATGAGCTAGGCACCTGTGTCCAGCTGCAGTGGCTCAGGGTGGTTG
ACACTCACTGTGGCTGGGCTGGGGTTCCACAGTGCTTTGAGATGTGCCTTTCTCAGCCCTGTACTGGTTCAAATATGAAC
TGGTGAAGAGCTGGCTGAACAGGCTCAAAAAACATGGCCAGACATCCATGGGT

Alignment

ORF - retro_itri_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.99 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VMTVPATAVY-FTAYDQLKT-FLCGQALTSDLYAPMVAGALARLGTVTVISPLELVRTKLQAQHVS-YRE
          VMTVP....Y..T.YDQ.K..FLC.QALTSDLYAP..AGA...LGTV..I.PLELV.TKLQ.QH.S.Y.E
Retrocopy VMTVPSMTIY<LTTYDQFKA<FLCRQALTSDLYAPIIAGAVTHLGTVRMIRPLELVQTKLQGQHAS>YHE

Parental  LGTCVR-AAVAQGGWRSLWLGWGPTALRDVPFSALYWFNYELVKRWLNGPRPKDQTSVG
          LGTCV..AAVAQGG..SLWLGWG.T.L.DVPFSALYWF.YELVK.WLN......QTS.G
Retrocopy LGTCVQ<AAVAQGG*HSLWLGWGSTVL*DVPFSALYWFKYELVKSWLNRLKKHGQTSMG

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_447 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_447 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447 ,