RetrogeneDB ID: retro_itri_800

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393325.1:6152809..6153058(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUTF2
• Ensembl ID: ENSSTOG00000002878
• Aliases: None
• Description: nuclear transport factor 2 [Source:HGNC Symbol;Acc:13722]

Sequence

>retro_itri_800
ATGGGAAACAGGCCAGTTTGGGAACAGATTGGATCCAGCTTCATTCAACATTACTACCAGTTATTAGATAATGACAGAAC
CGAACTAGGTGCAATTTATATTGACACATCACACCTAAAGTGGGAAGGGCAGCAGTTCCAGGGGACAGCTGCCATTGTGG
AGAAGTTGTCTAGCCTTCCGTTCCAGAAACTCCAGCCCAGAATCACTGCACAGGACCATCAGCCCACACTAGATAGCTGC
ATCATCAGC

Alignment

ORF - retro_itri_800 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 65.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLTSLPFQKIQHSITA
          MG..P.WEQIGSSFIQHYYQL.DNDRT.LGAIYID.S.L.WEGQQFQG.AAIVEKL.SLPFQK.Q..ITA
Retrocopy MGNRPVWEQIGSSFIQHYYQLLDNDRTELGAIYIDTSHLKWEGQQFQGTAAIVEKLSSLPFQKLQPRITA

Parental  QDHQPTPDSCIIS
          QDHQPT.DSCIIS
Retrocopy QDHQPTLDSCIIS

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_800 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_800 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 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Choloepus hoffmanni	ENSCHOG00000003059	3 retrocopies	retro_chof_1386, retro_chof_1619, retro_chof_2488,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Ictidomys tridecemlineatus	ENSSTOG00000002878	1 retrocopy	retro_itri_800 ,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,