RetrogeneDB ID: retro_itri_455

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393292.1:14007096..14007641(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC7
• Ensembl ID: ENSSTOG00000015164
• Aliases: None
• Description: armadillo repeat containing 7 [Source:HGNC Symbol;Acc:26168]

Sequence

>retro_itri_455
ATGGTCCAGAAGCCAAAGGTAGAACCCCATATCAGGCAGCTGGGGTATCTTTAGGCACTGGTTATGGAATTCCAGGAATC
TGAAAGCTGGGATGCCGAGTAGCAAGTCCTTGCCAATCTTGCCAGCTTTGCCTGTGACCCCTGCAAATACCAGTATCTGT
GACAACTACAAGTCCTGGATATATTGCTTGATTCTCTGTCAGAAGAGAATGAGAACCTGGTGGAGTTTGTTGTTAGGGGC
CTCTGCAACCTATGCTCAGACAGGACCAACAGGACCATAACTTGCATGCAGGCAGTATCCTGCTTGTCACCAACTGCTTG
TCCAATCCTAATGAGGAGACATTGTTGTCTGCAGTAACCATGCTCATATACCTGAGCTCACCAGGTGCCAGCTCCCACCC
TGAGCTGACTTCCATGCTGTTGGCCCAGTGCAGGCTGCACTTCTCTTTTTGAACCAACACAAGACTCCAGAATCTGGCCT
AGATCTTCCTGGAGGATTTCTGTTCCCCAAGTCAAATGGCAGAAGCTTGCAGCTGGCAAGCCCAC

Alignment

ORF - retro_itri_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.77 %
• Parental protein coverage: 91.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQKPKVDPHVGRLGYLQALVTEFQETESQDAKEQVLANLANFAYDPSNYQYLRQLQVVDLFLDSLSEEN
          M.QKPKV.PH...LGYL.ALV.EFQE.ES.DA..QVLANLA.FA.DP..YQYL.QLQV.D..LDSLSEEN
Retrocopy MVQKPKVEPHIRQLGYL*ALVMEFQESESWDAE*QVLANLASFACDPCKYQYL*QLQVLDILLDSLSEEN

Parental  ETLVEFAIGGLCNLCSDRTNK-DHILQAGGIPLITNCLSSPNEETVLSAVTTLMYLSSPGASSHPELTST
          E.LVEF...GLCNLCSDRTN..DH.L.AG.I.L.TNCLS.PNEET.LSAVT.L.YLSSPGASSHPELTS.
Retrocopy ENLVEFVVRGLCNLCSDRTNR<DHNLHAGSILLVTNCLSNPNEETLLSAVTMLIYLSSPGASSHPELTSM

Parental  PVVQCMLRFSLSANTRLRNLAQIFLEDYCSPSQVAEARSWQAH
          ...QC.L.FS...NTRL.NLA.IFLED.CSPSQ.AEA.SWQAH
Retrocopy LLAQCRLHFSF*TNTRLQNLA*IFLEDFCSPSQMAEACSWQAH

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_455 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_455 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000007172	1 retrocopy	retro_mdom_855,
Ictidomys tridecemlineatus	ENSSTOG00000015164	1 retrocopy	retro_itri_455 ,