RetrogeneDB ID: retro_itri_1810

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393858.1:127458..127812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSSTOG00000010557
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_itri_1810
TTTAAAAATTTATTGAAATTCTGTATTTTGTTTACTGGACTTTCAGTAGCCATTGGCATAATTCTGGTAAATGTATTTAT
TGGTTAAACTAAATTAGCAAAAGTTTTAGAAAATTATATTCTAGAATATTACAAGCATCCTATATCAAGATGGATTATTC
ATACTTTCTTTGACTACCCTGAAAAGAATTAAGAAAGAAAAATAGCTACTCTTCACATTGAATCTGAAAAGGATGCATTA
CATTTAAAGGAACTGGAAGTTGAAAGGGTAATTTGTGAGAGAAGCAATGAGCCCTGGTAACAATATTCAACTATTGACAA
GGCTCTTATTGATCATTCTTCAAAACAGCTTCCA

Alignment

ORF - retro_itri_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.29 %
• Parental protein coverage: 81.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLKLLRFYILLTGLPVAIGITLVNVFIGEAELAEIPEGYIPEHWEYYKHPISRWIARTFFDCPEKNYERT
          F..LL.F.IL.TGL.VAIGI.LVNVFIG...LA...E.YI....EYYKHPISRWI..TFFD.PEKN.ER.
Retrocopy FKNLLKFCILFTGLSVAIGIILVNVFIG*TKLAKVLENYI---LEYYKHPISRWIIHTFFDYPEKN*ERK

Parental  MAVLQIESEKAELRLKELEVRRLMRERGDGPWYQYPTPDKALIDHSPKATP
          .A.L.IESEK..L.LKELEV.R...ER...PW.QY.T.DKALIDHS.K..P
Retrocopy IATLHIESEKDALHLKELEVERVICERSNEPW*QYSTIDKALIDHSSKQLP

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_1810 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1810 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002684	1 retrocopy	retro_chof_1511,
Equus caballus	ENSECAG00000000682	1 retrocopy	retro_ecab_235,
Echinops telfairi	ENSETEG00000019363	1 retrocopy	retro_etel_1110,
Macropus eugenii	ENSMEUG00000014166	1 retrocopy	retro_meug_1852,
Myotis lucifugus	ENSMLUG00000000999	1 retrocopy	retro_mluc_2181,
Macaca mulatta	ENSMMUG00000009746	1 retrocopy	retro_mmul_2619,
Monodelphis domestica	ENSMODG00000021300	1 retrocopy	retro_mdom_1105,
Pongo abelii	ENSPPYG00000014493	2 retrocopies	retro_pabe_3018, retro_pabe_3796,
Pteropus vampyrus	ENSPVAG00000004286	1 retrocopy	retro_pvam_81,
Sorex araneus	ENSSARG00000006918	1 retrocopy	retro_sara_200,
Sus scrofa	ENSSSCG00000011764	1 retrocopy	retro_sscr_193,
Ictidomys tridecemlineatus	ENSSTOG00000010557	1 retrocopy	retro_itri_1810 ,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,