RetrogeneDB ID: retro_itri_705

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393313.1:5248980..5249436(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNGR2
• Ensembl ID: ENSSTOG00000006834
• Aliases: None
• Description: synaptogyrin 2 [Source:HGNC Symbol;Acc:11499]

Sequence

>retro_itri_705
GCCATCGGCCTGCTGGCCTTCCCAGCCTCAGCCTTCTTCTTTGTGGTTGATGCCTATTTTCCCTAGACCAGCAATGCCAC
TGACCACAAGTACCTGGTCACTGGCGACCTGCTCTTCTCAGCTCTCTGAACCTTCCTATGGTTTGTTAGTTTCTGCTTCC
TCACCAACCAATGGGCAGCCACCAAGCTGGAAGATGTGTTGGTGGGAGCTGACTCGACTCAGGCAATGATCTCTTTCAGC
TTCTTCTCTGTCTTCTCCTGGGGCACACTGGCTTCCCTGGCCTACCAGCGCTACATGGCTGCAGTGGACACCTTTATCCT
GAACTATGTAGACCCCACCCCAGACCCCAACACGGCCTACACCTCCTACTCCAGCGCATCAGTGGATAACTACCAGCACC
CACCCTTCACTCAGAGTGTGGACACCACTGAGGGCTACCAGCCGCCCACTGTGTAC

Alignment

ORF - retro_itri_705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 79.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVGVLAFLASAFFFVVDVYFPQISSATDRKYLVIGDLLFSALWTFLWFVGFCFLTNQWAATKLEDVLVGA
          A.G.LAF.ASAFFFVVD.YFP..S.ATD.KYLV.GDLLFSAL.TFLWFV.FCFLTNQWAATKLEDVLVGA
Retrocopy AIGLLAFPASAFFFVVDAYFP*TSNATDHKYLVTGDLLFSAL*TFLWFVSFCFLTNQWAATKLEDVLVGA

Parental  DSARAAITFSFFSIFSWGALASLAYQRYKAGVDAFIQNYVDPTPDPNTAYASYPSASVDNYQQPPFTQSA
          DS..A.I.FSFFS.FSWG.LASLAYQRY.A.VD.FI.NYVDPTPDPNTAY.SY.SASVDNYQ.PPFTQS.
Retrocopy DSTQAMISFSFFSVFSWGTLASLAYQRYMAAVDTFILNYVDPTPDPNTAYTSYSSASVDNYQHPPFTQSV

Parental  ETTEGYQPPAVY
          .TTEGYQPP.VY
Retrocopy DTTEGYQPPTVY

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_705 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_705 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108639	2 retrocopies	retro_hsap_1472, retro_hsap_4275,
Macaca mulatta	ENSMMUG00000021864	1 retrocopy	retro_mmul_1200,
Pongo abelii	ENSPPYG00000008684	2 retrocopies	retro_pabe_1220, retro_pabe_3487,
Ictidomys tridecemlineatus	ENSSTOG00000006834	1 retrocopy	retro_itri_705 ,