RetrogeneDB ID: retro_itri_1392

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393472.1:2028034..2028458(+)
• Located in intron of: ENSSTOG00000016252

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYM6NB
• Ensembl ID: ENSSTOG00000020434
• Aliases: None
• Description: ZMYM6 neighbor [Source:HGNC Symbol;Acc:40021]

Sequence

>retro_itri_1392
CTGCTGGGTGGCTTCTTTGTACTCATGGGTTGGCCAAGCTCTCGCAGATCTCTGCTCTTGTGTCACAGCAGAGGAAAGCC
CTGTTGCTGCAGTTTGCTAAGGTGTTCGCATTGAAGTTGTTCGGCTACCAGTCAGATCCTGTGAGCTACCCAACAGCTGT
GGGCTGGCTGGAGCTGCTGGCTGGGTGGCTGTTGGTTGTGGGCCCACCAGTTCTACAAGATATCAGTAACTTGCTCTTGA
CCCTCCCCACGATGGTGGCTGTCTTCACTATGGCATCTCTGAAAGAGTCACTGAGGTCTCCATCCCAGCCATCATCTGCT
TGGGGCTCCTGCTGTTGCTGGACATCTGCCAGTTCTTAGCCCAAGCCAAGAATGTGGTCATACACTCTAGGAAGAAGACT
CCGAGTGCATTCAAGGAACCCTGG

Alignment

ORF - retro_itri_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.86 %
• Parental protein coverage: 92.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLGGFFALTG-AAKLSQISAPVSQQMKALFVQFAEVFPLKLFGYQPDPVNYQTAVGWLELLAGLLLVVGP
          LLGGFF.L.G..AKLSQISA.VSQQ.KAL..QFA.VF.LKLFGYQ.DPV.Y.TAVGWLELLAG.LLVVGP
Retrocopy LLGGFFVLMG<LAKLSQISALVSQQRKALLLQFAKVFALKLFGYQSDPVSYPTAVGWLELLAGWLLVVGP

Parental  PVLQDISNFLLTLLMMVAIFTLVSLKESL-STSIPAIVCLGLLLLLDVCQFLAQTKKMVRHSRKKTPSAF
          PVLQDISN.LLTL..MVA.FT..SLKESL...SIPAI.CLGLLLLLD.CQFLAQ.K..V.HSRKKTPSAF
Retrocopy PVLQDISNLLLTLPTMVAVFTMASLKESL<EVSIPAIICLGLLLLLDICQFLAQAKNVVIHSRKKTPSAF

Parental  KEPW
          KEPW
Retrocopy KEPW

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_1392 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1392 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000020434	1 retrocopy	retro_itri_1392 ,