RetrogeneDB ID: retro_itri_1314

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393437.1:4564485..4564987(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023538
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSSTOG00000020292
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_itri_1314
ATAGCTGCATATCCTCACAAATATCAGAATTTCTTAACCCTACACAAAGTCATCATGAAGAGCAGTGGTGATACGGGCAA
ATCTGTTGGGACTCTACAGTTCATGTACGAGGAGTTTGTGGAGGACTCTGAACCTAGCAAAGCAGAGAGCTATAGGAAGA
AGGTGTGCTGGATGGGGAGGAAGTGTACATCTCCACAACTCAGAGCAGCTAAACAGGAAGACCAAGCTGCAATTGGAGAC
AACTGCTTCCATATGGAGGAGGAGTTCCTCTGTACCTTCTTGACTGCAGAAATGCAATTGTTGGCAACCACAGCTGGCTT
CAAGGAGGATATTTTAAGAGGAAAAAAAGATGAGAATCTTTCATTTCTACTGGTTGGTAACAGATTAAATTTGAAAGATA
AAAAGGCAGGTTTCTATAGAAAAGGCAAAAAAGAGAGCTGGCCAGTGGAAGGATAAGTATGTGGAAACTTCTGCTAAAAT
ATGAGCTAATGTTGATAATGTC

Alignment

ORF - retro_itri_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.53 %
• Parental protein coverage: 81.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKV-VLDGEEVQIDI-LD
          .AA...K.QN.L.LHKVIM..SG..GKS..TLQFMY.EFVED.EP.KA.SYRKKV.VLDGEEV.I...L.
Retrocopy IAAYPHKYQNFLTLHKVIMKSSGDTGKSVGTLQFMYEEFVEDSEPSKAESYRKKV<VLDGEEVYIST>LR

Parental  TAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLED-KRQV
          .A.QED.AAI.DN.F...E.FLC.F...EM...A.TA.F.E.ILR.K.DEN..FLLVGN...L.D.KRQV
Retrocopy AAKQEDQAAIGDNCFHMEEEFLCTFLTAEMQLLATTAGFKEDILRGKKDENLSFLLVGNRLNLKD>KRQV

Parental  SVEEAKNRADQWNVNYVETSAKTRANVDKV
          S.E.AK.RA.QW...YVETSAK..ANVD.V
Retrocopy SIEKAKKRAGQWKDKYVETSAKI*ANVDNV

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_1314 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1314 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314 , retro_itri_1315,
Ictidomys tridecemlineatus	ENSSTOG00000021028	1 retrocopy	retro_itri_84,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,