RetrogeneDB ID: retro_itri_1843

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394043.1:10624..11227(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf41
• Ensembl ID: ENSSTOG00000000385
• Aliases: None
• Description: chromosome 9 open reading frame 41 [Source:HGNC Symbol;Acc:23435]

Sequence

>retro_itri_1843
GGACTGGGAATTAGCTGTGCTAGGTGATCCTTGTCAAGGATAGGAATTAAGTGTTCTTGTTGTTGTTGTTGTTGTTTTAG
GCTCTTTTATCTCAACCTTGTTCTGAACAGATGTTCTAAAATTAATAAACATACACTTTATTCCTGGATCTACCTGTTTA
GCAATAATGGGAGATCAGAAGATCAGATGCCACCCATTTTTTTCCTGATATTGACCCCCACAGTCTTCCTCCTGGTTCTA
AATTTTGTTTGACAGCAGAAGATTTTCAGGAGATTTATTCATAATGCAGTAGGTGGCACTATATTGCCCCCTGTTTCTGC
ATAGGCACAGCTCACAATGTAATTGACTATATTGACACAATATGAAACACATTCAAGCCAGGTGAATTTTGATAAATCTT
GGTTCTCTGCTGTACTACTTTGAAAATTTGGCAAAAAATTTTCCATAGAATTGAGCTATGAGGATATAAACAATGTTGTT
CTGCAAAATAGATTCCAGGTACAGGTGGACAAAGAATCCGTATTGTCAACATAGACTGTGAAGGATTTCTCTATGATGAA
ATACTATTATGAATTTGTCTTATTTGTAGTTCATAAGCCACAA

Alignment

ORF - retro_itri_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.9 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAGLGRLAWEIAMLGYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPIFF-P
          G.G...........G............LF..N.VLNRCS.INK..LY.WI..FSNN.RS.DQ..PIFF.P
Retrocopy GLGISCAR*SLSRIGIKXXXXXXXXXRLFYLNLVLNRCSKINKHTLYSWIYLFSNNGRSEDQMPPIFF<P

Parental  DVDPHSLPPGSNFSMTAGDFQEIYSECNTWDCIATCFFIDTAHNVIDYIDTIWKILKPGG-IWINLGPLL
          D.DPHSLPPGS.F..TA.DFQEIYS.C..W..IA.CF.I.TAHNVIDYIDTI....KPG..I.INLG.LL
Retrocopy DIDPHSLPPGSKFCLTAEDFQEIYS*CSRWHYIAPCFCIGTAHNVIDYIDTI*NTFKPGE<ILINLGSLL

Parental  YHFENLA-NELSIELSYEDIKNVVLQYGFQVEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ
          Y.FENLA....SIELSYEDI.NVVLQ..FQV.V.KESVLST.TV.D.SMMKYYYE.VLFVV.KPQ
Retrocopy YYFENLA<KKFSIELSYEDINNVVLQNRFQVQVDKESVLST*TVKDFSMMKYYYEFVLFVVHKPQ

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_1843 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1843 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 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024726	2 retrocopies	retro_mmus_1013, retro_mmus_3359,
Oryctolagus cuniculus	ENSOCUG00000017017	4 retrocopies	retro_ocun_1659, retro_ocun_1737, retro_ocun_1827, retro_ocun_921,
Ictidomys tridecemlineatus	ENSSTOG00000000385	5 retrocopies	retro_itri_1389, retro_itri_1652, retro_itri_1653, retro_itri_1654, retro_itri_1843 ,