RetrogeneDB ID: retro_itri_1713

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393652.1:639618..640029(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024195
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMA6
• Ensembl ID: ENSSTOG00000011774
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 6 [Source:HGNC Symbol;Acc:9535]

Sequence

>retro_itri_1713
ATGTCCCATGGTTCCAGCGCTGGTTTTGACCGCCACATTACCATTTTTTCGCCCGAAGGCCGGCTTTACCAAGTAGAATA
TGCTTTTAAGGCTATAAACCAGGGTGGTCTGACATCAGTAGCTGTCAGAGGGAAAGACTGTGCAGTAATTGTCACACAGA
AGAAAGTACCTGACAAATTATTGGATTCCAGCACAGTGACTCACTTATTCAAGATAACTGAAAATGTTGGCTGTGTGATG
ACTGAAATGACAGCTGACAGCAGATCCCAGGTACAAAGGGCACGCTATGAAGCAGCTAATTGGAAATACAAGTATGGCTA
TGAGATTCCTGTGAACATGCTGTGTAAAAGAATTGCTGATATTTCTCAGGTCTACACACAGAATGCTGAAATGAGGCCAC
TTGGTTGTTGT

Alignment

ORF - retro_itri_1713 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
          MS.GSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
Retrocopy MSHGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF

Parental  KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCC
          KITEN.GCVMT.MTADSRSQVQRARYEAANWKYKYGYEIPV.MLCKRIADISQVYTQNAEMRPLGCC
Retrocopy KITENVGCVMTEMTADSRSQVQRARYEAANWKYKYGYEIPVNMLCKRIADISQVYTQNAEMRPLGCC

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_1713 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1713 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004892	1 retrocopy	retro_etel_1775,
Macropus eugenii	ENSMEUG00000016537	1 retrocopy	retro_meug_1217,
Macaca mulatta	ENSMMUG00000016544	1 retrocopy	retro_mmul_343,
Rattus norvegicus	ENSRNOG00000007114	4 retrocopies	retro_rnor_1724, retro_rnor_1960, retro_rnor_854, retro_rnor_924,
Ictidomys tridecemlineatus	ENSSTOG00000011774	1 retrocopy	retro_itri_1713 ,