RetrogeneDB ID: retro_itri_634

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:8042316..8042700(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRGBP
• Ensembl ID: ENSSTOG00000012953
• Aliases: None
• Description: MRG/MORF4L binding protein [Source:HGNC Symbol;Acc:15866]

Sequence

>retro_itri_634
CCCGTGCAGGTAAACCAATGCTTCCTCATGATTTGTATCCCTGACAAATTCAGCCAGAATATTGGGAGGTAAGCCCCATC
CAAGGTCATCTGGGACCATCGGAGCACCATTTACAACATGAAGGCACTACATGAATCTGAGATTCTTCCATTCCCGAATC
CAGAGAGGAACTTTGTCCTTCCAGAAGAGATCATTCAGGAAGTCTGAGAAGGAAAAGTGGTCCGTGAAGAGGAAATGAAG
GAGGAGATGAAGGAAGATGTGGACCCCCACAGGGGGCTGCCGACATCTTCAGGAAACTTGGGGACATCAACAGGAAAATC
CAGCAAAGAGAAGAGCTCCTCAGACTTTGGGTGTAAAGACAGGGGCCAAGCAGAAGCACAAAGT

Alignment

ORF - retro_itri_634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 84.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTGVNRHFHMICIRDKFSQNIGRQVPSKVIWDHLSTMYDMQALHESEILPFPNPERNFVLPEEIIQEVRE
          P..VN..F.MICI.DKFSQNIGR..PSKVIWDH.ST.Y.M.ALHESEILPFPNPERNFVLPEEIIQEV.E
Retrocopy PVQVNQCFLMICIPDKFSQNIGR*APSKVIWDHRSTIYNMKALHESEILPFPNPERNFVLPEEIIQEV*E

Parental  GKVVIEEEMKEEMKEDVDPHSGADDVFSSSGSLGKSTEKSSKDKEKSSSDLGCKDGADKRKRS
          GKVV.EEEMKEEMKEDVDPH.G......SSG.LG.ST.KSS..KEKSSSD.GCKD.......S
Retrocopy GKVVREEEMKEEMKEDVDPHRGLP---TSSGNLGTSTGKSS--KEKSSSDFGCKDRGQAEAQS

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_634 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_634 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020272	1 retrocopy	retro_cpor_1438,
Monodelphis domestica	ENSMODG00000016803	1 retrocopy	retro_mdom_246,
Mus musculus	ENSMUSG00000027569	1 retrocopy	retro_mmus_1383,
Sarcophilus harrisii	ENSSHAG00000010685	1 retrocopy	retro_shar_128,
Ictidomys tridecemlineatus	ENSSTOG00000012953	1 retrocopy	retro_itri_634 ,