RetrogeneDB ID: retro_itri_183

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01149321.1:703..1510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026572
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011341
• Aliases: None
• Description: None

Sequence

>retro_itri_183
AGAGCAGACCGTTTATGAGCTTCAGGAAAATACCAAGAGGCTATTTCTTGTCACAAGAAGGCTACGGCCTATCTTTCTGA
TGCTCTGAAGCTGACCAAGTCTGAGCAGGCTCATTTATCACTGCAATTAAAAGGGGATAGCCACATGGAACAGCTTCTCC
TCATCCAGGAGAGGTGGAAAAGGGCAAAGTGTGAAGAACTATCAAAAGCTCAGAACACAGACAAGGATGTAGCCACCCAT
TTTCAGGCATCTCACAAACCCTCTACTGAGGTTGCAGAGGCTCAGAGTCCCCTTCTTTCTCAGAACTACAGCCCTTGTAC
AGAGAAACACCTCTCTGAAATTCAGGGAGTCTTTGACAGGAATACAGAAACACTACTATTTTTACTTCAGCAAAAGAGTG
AGACAACACAGCCATGTATTGGAAGCAAAGCCCCGAAGGATGATAAAATAATTATTGAGAAGCAGGCAACCAAAATTGCA
AATTTGAAAATGTATGAGGAGTTCCTTGTGGCTGAAAATGAAAGATTAAGGAAAGAAAATAAAGCACTAAAGGCTGAAAA
AGCCAGACTTGTAAAAGTTCCAGTAGATAAGGAGCTGGATGTGGATACTGATTTTATAGAAAAGTCAGCATTATGGAACT
TGCCACCACATTCAGACACTGCTACACCTTCAACCTGGCAGAAATTTGCAGCAAATACTGGGAAAGACAAGGATATTCCA
ATACCCAATCTTCCTCCCTTGGATTTTCCATCTCCACAACTTCCACTTATGGAGTTGTCTGAGGATTTTCTGGAAGGACT
TACGAAT

Alignment

ORF - retro_itri_183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 94.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RADRLLAAGKYEEAISCHKKAAAYLSDAMKLTKSEQAHLSLELQRDSHMKQLLLIQERWKRAKREERSKA
          RADRL.A.GKY.EAISCHKKA.AYLSDA.KLTKSEQAHLSL.L..DSHM.QLLLIQERWKRAK.EE.SKA
Retrocopy RADRL*ASGKYQEAISCHKKATAYLSDALKLTKSEQAHLSLQLKGDSHMEQLLLIQERWKRAKCEELSKA

Parental  QNTDKDVATHLQASHKPSAEEAEGQSPLLSQKYSPSTEKHLPEIQGVFDRDPDTLLFLLQQKSEPTEPCI
          QNTDKDVATH.QASHKPS.E.AE.QSPLLSQ.YSP.TEKHL.EIQGVFDR...TLLFLLQQKSE.T.PCI
Retrocopy QNTDKDVATHFQASHKPSTEVAEAQSPLLSQNYSPCTEKHLSEIQGVFDRNTETLLFLLQQKSETTQPCI

Parental  GSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGPVDKELDVDADFVEKSE
          GSKAPKDDK.IIE.QATKIA.LK...EFLVAENERLRKENK.LKAEKARL.K.PVDKELDVD.DF.EKS.
Retrocopy GSKAPKDDKIIIEKQATKIANLKMYEEFLVAENERLRKENKALKAEKARLVKVPVDKELDVDTDFIEKSA

Parental  LWSLPPHSDTATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDFLKGLMN
          LW.LPPHSDTAT..STWQKFAANTGK.KDIPIPNLPPLDFPSP.LPLMELSEDFL.GL.N
Retrocopy LWNLPPHSDTAT-PSTWQKFAANTGKDKDIPIPNLPPLDFPSPQLPLMELSEDFLEGLTN

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_183 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_183 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183 ,