RetrogeneDB ID: retro_itri_413

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:550774..551184(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSSTOG00000028067
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 9 [Source:HGNC Symbol;Acc:19123]

Sequence

>retro_itri_413
GGTTCTGAAGAAGAACTGGCTGGTACTAAACAGGCCACCTATCTGGATTTCAAGGGGATCAGATCATGGAGTCTGTACTT
TGTGTGCAGTACATAGAGAAACCCAGGATAAGGAACATTCAGCAAGCTATCCACAACAAAGAAAGCCCATCCTATAATGC
CTTTGTTAAAACATCAAAACAAAAGATGAATACAAAGAAAAGGAGAGTTCAGGAGGAAGCTAAAGAAGCAAAAATGAACA
GGAAGGAGTTGGGCCTTAACGAAGAAGTGGATAACTTGAAAGCACTCATTCAGGGTAGACAAAAGGATCAGCAAAAGGAA
ATGGGCAATTTTCTGGCTCAGATGGAAGCAAAATTCTGCAAACCTTCCAAAGGAGGAGGGAAAAGATCAATTCTCAAGAA
AGAAAAGAAA

Alignment

ORF - retro_itri_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 53.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSEEELADIKQA-YLD-FKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAKEVPSYNAFVKESKQKMNAR
          GSEEELA..KQA.YLD.F.GD..QIMESVLCVQY.E.PRIRNI.QQAI..KE.PSYNAFVK.SKQKMN..
Retrocopy GSEEELAGTKQATYLD<FQGD--QIMESVLCVQYIEKPRIRNI-QQAIHNKESPSYNAFVKTSKQKMNTK

Parental  KRRAQEEAKEAEMSRKELGLDEGVDNLKALIQSRQKDRQKEMDNFLAQMEAKYCKPSKGGGKRSALKKEK
          KRR.QEEAKEA.M.RKELGL.E.VDNLKALIQ.RQKD.QKEM.NFLAQMEAK.CKPSKGGGKRS.LKKEK
Retrocopy KRRVQEEAKEAKMNRKELGLNEEVDNLKALIQGRQKDQQKEMGNFLAQMEAKFCKPSKGGGKRSILKKEK

Parental  K
          K
Retrocopy K

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_413 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_413 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016933	1 retrocopy	retro_amel_478,
Felis catus	ENSFCAG00000004448	1 retrocopy	retro_fcat_1310,
Homo sapiens	ENSG00000213551	2 retrocopies	retro_hsap_1358, retro_hsap_2448,
Gorilla gorilla	ENSGGOG00000015046	3 retrocopies	retro_ggor_1058, retro_ggor_1499, retro_ggor_1524,
Myotis lucifugus	ENSMLUG00000004539	3 retrocopies	retro_mluc_699, retro_mluc_700, retro_mluc_955,
Mustela putorius furo	ENSMPUG00000003792	1 retrocopy	retro_mputfur_727,
Nomascus leucogenys	ENSNLEG00000016595	1 retrocopy	retro_nleu_1394,
Otolemur garnettii	ENSOGAG00000003496	2 retrocopies	retro_ogar_1730, retro_ogar_1740,
Pongo abelii	ENSPPYG00000002343	2 retrocopies	retro_pabe_1126, retro_pabe_1799,
Pan troglodytes	ENSPTRG00000034219	2 retrocopies	retro_ptro_1414, retro_ptro_931,
Ictidomys tridecemlineatus	ENSSTOG00000028067	1 retrocopy	retro_itri_413 ,
Tarsius syrichta	ENSTSYG00000011504	1 retrocopy	retro_tsyr_39,