RetrogeneDB ID: retro_itri_388

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:20049409..20050398(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000015205
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004003
• Aliases: None
• Description: None

Sequence

>retro_itri_388
ATGAGCCCAGGGCGTGGAAAATATGATTTCTGTATTGGTTTGGCATTGGCTATGACCTCCAGCATTTTCATAGGAGGGAG
TTTCATTTTGAAAAAAAAAAAAAAAGACCTTCTGCGACTTGCCAGAAAAGGACCCATGAGAGCAGGTCAAGGTGGCCATG
CATATCTTAAAGAATGGTTGTGGTGGGCTGGACTACTGTCAATGGGGGCAGTCGAGGTGGCCAACTTCGCTGCATGTGCC
TTTGCACCAGCCACGCTAGTGACTCCACTGGGAGCTCTCAGCGTCCTCGTAAGTGCCATTCTTTCTTCATACTCTCTAAA
TGAAAGACTTAATCTTCATGGGAAAATTAGATGTTTGCTAAGCATTCTAGGATCTACAGTTATGGTCATCCATGCTCCAA
AGGAAGAGGAGATTGAGATGTTAATTGAAATGTCACACAAGTTAGGTGATCCAGGTTTCGTGGTATTTGCAACAATTGTG
GTCATTGTGTCCTTGATATTAATCTTTGTGGTGGGACCTCGCCACGGACAGACAAATATTCTTGTGTACATAACAATCTG
CTCTGTGATCGGGGTGTTTTCAGTGTCCTGTGCAAAGGGCATGGGCATCACCATAAAAGAACTGTTAGCTGGAAAGCGTG
GGCTGCGGCATCCCCTGGCCTGGATTCTGCTGCTGAGCCTCGTCATCTGTGTGAGCACACAGATCAATGACCTAAACCGG
GCCCTGGACATATTCAACACTTCCCTTGTAACACCAATATATTACGTTTTCTTTACAACCTCAGTTCTAACTTGTTCAGC
TATTCTTTTTAAGGAGTGGCAAGATATGCCTGCTGATGATATCATTGGGACTCTGAGTGGCTTCTTTACAATCATGTGGG
GATATTCTTGTTGCGTGCCTTTAAAGATGTCAGCTTTAGTCTAGCAAGTCTGCCTGTCTCTTTTCGAAAAGATGATAAAG
CAATGAATGTTAACCTCCCTACTATGTAT

Alignment

ORF - retro_itri_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 91.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSPGRGKYDFYIGLGLAMTSSIFIGGSFILKKKG--LLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGA
          MSPGRGKYDF.IGL.LAMTSSIFIGGSFIL......LLRLARKG.MRAGQGGHAYLKEWLWWAGLLSMGA
Retrocopy MSPGRGKYDFCIGLALAMTSSIFIGGSFILXXXXXDLLRLARKGPMRAGQGGHAYLKEWLWWAGLLSMGA

Parental  GEVANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIET
          .EVANFAA.AFAPATLVTPLGALSVLVSAILSSY.LNERLNLHGKI.CLLSILGSTVMVIHAPKEEEIE.
Retrocopy VEVANFAACAFAPATLVTPLGALSVLVSAILSSYSLNERLNLHGKIRCLLSILGSTVMVIHAPKEEEIEM

Parental  LNEMSHKLGDPGFVVFATIVVIVSLILIFVVGPRHGQTNILVYITICSVIGAFSVSCAKGLGITIKELLA
          L.EMSHKLGDPGFVVFATIVVIVSLILIFVVGPRHGQTNILVYITICSVIG.FSVSCAKG.GITIKELLA
Retrocopy LIEMSHKLGDPGFVVFATIVVIVSLILIFVVGPRHGQTNILVYITICSVIGVFSVSCAKGMGITIKELLA

Parental  GKPVLRHPLAWILLLSLVICVSTQINYLNRALDIFNTSLVTPIYYVFFTTSVLTCSAILFKEWQDMPADD
          GK..LRHPLAWILLLSLVICVSTQIN.LNRALDIFNTSLVTPIYYVFFTTSVLTCSAILFKEWQDMPADD
Retrocopy GKRGLRHPLAWILLLSLVICVSTQINDLNRALDIFNTSLVTPIYYVFFTTSVLTCSAILFKEWQDMPADD

Parental  IIGTLSGFFTII-VGIFLLHAFKDVSFSLASLPVSFRKDDKAMNGNLPTMY
          IIGTLSGFFTI..VGIFLL.AFKDVSFSLASLPVSFRKDDKAMN.NLPTMY
Retrocopy IIGTLSGFFTIM<VGIFLLRAFKDVSFSLASLPVSFRKDDKAMNVNLPTMY

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_388 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_388 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388 ,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,