RetrogeneDB ID: retro_itri_537

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393299.1:10123705..10124151(-)
• Located in intron of: ENSSTOG00000006169

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSSTOG00000002828
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_itri_537
ATGGAAGGCCACAGGGTGAGTTTACCATTATTCCTGTACCAGTTGGAGCTCTGAGTGAGTCAAAAGAACAGGAATTTAGA
AAACTCTTCAGTAAATATCTAGCAGATCTTAATAATCTCTTTGTGGTTTCTCTGATTTCTGCCACTAGGATCAAAGGTTG
TTACAGTTCCTATGATGAATCCTGGGAGGAGATTTATAGATCCATTGAACATCTAGATAAAAGAGGTATGAGTATTATAG
AATAATCATATCATGTATCTTTTAGCCATTACTTGAAGAAACACCATAATACTATATGTGGAAGGCATCCCATTAGGTTG
TTATTAAATGCTATCACAGAGCTCCAGAAGAATGAAATGAATATGAGCTTTTCCTTTTTGAATTATGCCCAGTCAAGCGA
GTGTAGTTCTGCCTTGAGTTATGTAGCTGGAGCACTCACAGTCCAC

Alignment

ORF - retro_itri_537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MESHK-DEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVS-SDFCHWGQRFRY-SYYDESQGEIY
          ME.H...EFTIIPV.VGALSESKEQEF.KLFSKYLAD..NLFVVS.SDFCH..QR....SY.DES..EIY
Retrocopy MEGHR<GEFTIIPVPVGALSESKEQEFRKLFSKYLADLNNLFVVS<SDFCH*DQRLLQ>SY-DESWEEIY

Parental  RSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNGMNMSFSFLNYAQSSQCR
          RSIEHLDK.GMSIIE....VSFS.YLKK.HNTICGRHPI..LLNAITELQKN.MNMSFSFLNYAQSS.C.
Retrocopy RSIEHLDKRGMSIIE*SYHVSFSHYLKKHHNTICGRHPIRLLLNAITELQKNEMNMSFSFLNYAQSSEC-

Parental  NWQDSSVSYAAGALTVH
          ....S..SY.AGALTVH
Retrocopy ---SSALSYVAGALTVH

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_537 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_537 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Ictidomys tridecemlineatus	ENSSTOG00000002828	2 retrocopies	retro_itri_1321, retro_itri_537 ,