RetrogeneDB ID: retro_itri_57

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:8133902..8134442(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021489
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000013678
• Aliases: None
• Description: None

Sequence

>retro_itri_57
ATGAACTCGATTTTATCGCGGGCGAACTCACTGTTCGCTTTCTCGCTGAGCGTGATGGCGGCGCTCACCTTGGGCTGCTT
CATCACCACAGCTTTCAAAGACAGGAGCGCCCCGGTGCGTTTGCACGTTTCGCGGATCCTGCTGAAAAATGTAGAAGACT
TCACTGGACCCAGAAAAAGAAGTGATCTGGGATTCATTACATTTCATATCACTGCGGATCTGGAGAATACTTTCGATTGG
AATGTTAAGCAGCTGTTTGTTTATTTATCAGCGGAATATTCAACAAAAAATAATGCTGTGAATCAAGTGGTCCTTTGGGA
CAAGATTGTTCTGAGAGGTGATAATCCGAAGCTGCTATTGAAAGATATGAAGACAAAATATTTTTTCTTTGATGATGGAA
ATGGTCTCAAGGGAAACAGGAATGTCACTTTGACCTTATCTTGGAACGTTGTACCAAATGCTGGAATTCTGCCTCTTGTG
ACAGGAACAGGACGTGTATCTGTCCCATTTCCAGATGCATATGAAATAACCAAGAGTTAT

Alignment

ORF - retro_itri_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNTVLSRANSLFAFSLSVMAALTFGCFITTAFKDRSVPVRLHVSRIMLKNVEDFTGPRERRNIYFLFLRF
          MN..LSRANSLFAFSLSVMAALT.GCFITTAFKDRS.PVRLHVSRI.LKNVEDFTGPR.R....F.....
Retrocopy MNSILSRANSLFAFSLSVMAALTLGCFITTAFKDRSAPVRLHVSRILLKNVEDFTGPRKRSDLGFITFHI

Parental  GGHVKNIFDWNVKQLFLYLSAEYSTKNNALNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR
          .....N.FDWNVKQLF.YLSAEYSTKNNA.NQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR
Retrocopy TADLENTFDWNVKQLFVYLSAEYSTKNNAVNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR

Parental  NVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTYEITKSY
          NVTLTLSWNVVPNAGILPLVTG.G.VSVPFPD.YEITKSY
Retrocopy NVTLTLSWNVVPNAGILPLVTGTGRVSVPFPDAYEITKSY

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_57 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_57 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001987	2 retrocopies	retro_mmur_1595, retro_mmur_731,
Oryctolagus cuniculus	ENSOCUG00000029741	1 retrocopy	retro_ocun_119,
Otolemur garnettii	ENSOGAG00000003825	1 retrocopy	retro_ogar_1710,
Pongo abelii	ENSPPYG00000015218	1 retrocopy	retro_pabe_138,
Sarcophilus harrisii	ENSSHAG00000015012	1 retrocopy	retro_shar_481,
Ictidomys tridecemlineatus	ENSSTOG00000013678	1 retrocopy	retro_itri_57 ,