RetrogeneDB ID: retro_itri_1866

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394274.1:66156..66714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC28
• Ensembl ID: ENSSTOG00000004380
• Aliases: None
• Description: leucine rich repeat containing 28 [Source:HGNC Symbol;Acc:28355]

Sequence

>retro_itri_1866
ATGGCATCCGAACTTTGTAAGATGATCACTGTGGCAAGGCTTGAAAAGCACAAGAATTTGTTCTTAAATTATAGGAATCT
GCACCATTTTCCATTGGAGTTACTGAAAGATGAAGGACTGCAGTACTTGGAGAGACTCTGTATGAAAAGGAACTCCCTTA
CCACCTTGCCATAAAACCTTGCTCAGAAGCTTCCAAACCTTGTGAAACTGTATCTTCACTCAAATAACATAGTAGTGGTT
CCAGAAGCTATTGGGTTCCTTGTAAAACTCCAGTATCTGGGTCTTAGTGATAATGTCTTAGAAATTGTTTGCCCAGATAT
TGGTCATCTGAGAGCTTTACTTCATCTTCGATTAGCTAATAATCAACTGCAATTCCTACCTCCAGAGGTTGGTGATTTGA
AGGAGCTGCAGATACTAGATATTTCTACCAATCGTCTGCTAACTTTACCCGAGAGGCTTCATCTGTGCCTTTCTCTGCAG
TACCTCACTGTGGACGGAAATCGTCTATGGTATGTGCCGCACCGTCTCTGCCAGCTTCCCAGCCTCAACAAACTCTCT

Alignment

ORF - retro_itri_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASELCKTITVARLEKHKNLFLNYRNLHHFPLELLKDEGLQYLERLYMKRNSLTTLPENLAQKLPNLVEL
          MASELCK.ITVARLEKHKNLFLNYRNLHHFPLELLKDEGLQYLERL.MKRNSLTTLP.NLAQKLPNLV.L
Retrocopy MASELCKMITVARLEKHKNLFLNYRNLHHFPLELLKDEGLQYLERLCMKRNSLTTLP*NLAQKLPNLVKL

Parental  YLHSNNIVVVPEAIGSLVKLQYLDLSDNALEIVCPEIGRLRALRHLRLANNQLQFLPPEVGDLKELQTLD
          YLHSNNIVVVPEAIG.LVKLQYL.LSDN.LEIVCP.IG.LRAL.HLRLANNQLQFLPPEVGDLKELQ.LD
Retrocopy YLHSNNIVVVPEAIGFLVKLQYLGLSDNVLEIVCPDIGHLRALLHLRLANNQLQFLPPEVGDLKELQILD

Parental  ISTNRLLTLPERLHLCLSLQYLTVDRNRLWYVPRHLCQLPSLNELS
          ISTNRLLTLPERLHLCLSLQYLTVD.NRLWYVP..LCQLPSLN.LS
Retrocopy ISTNRLLTLPERLHLCLSLQYLTVDGNRLWYVPHRLCQLPSLNKLS

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_1866 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1866 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016965	1 retrocopy	retro_cjac_2430,
Erinaceus europaeus	ENSEEUG00000006720	1 retrocopy	retro_eeur_672,
Monodelphis domestica	ENSMODG00000012729	1 retrocopy	retro_mdom_1822,
Ictidomys tridecemlineatus	ENSSTOG00000004380	1 retrocopy	retro_itri_1866 ,