RetrogeneDB ID: retro_itri_174

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393393.1:2975603..2976248(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020857
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSSTOG00000011857
• Aliases: None
• Description: ribosomal protein L10 [Source:HGNC Symbol;Acc:10298]

Sequence

>retro_itri_174
ATGGGCCGCCGCCCTGCTCGCTGTTACCGGTATTGTAAGAACAAGCCTTACCCAAAGTCTCGTTTCTGCCGAGGTGTCCC
AGATGCCAAGATTCGCATCTTTGACCTGGGTCGGAAAAAGGCGAAAGTGGATGAGTTCCCACTCTGTGGTCACATGGTGT
CCGATGAGTACGAGCAGCTGTCCTCCGAAGCCCTGGAGGCCGCCCGCATCTGCGCCAACAAGTACATGGTGAAAAGTTGT
GGCAAAGATGGCTTTCACATTCGAGTACGCCTCCATCCTTTCCATGTCATCCGTATCAACAAGATGTTGTCCTGTGCTGG
GGCTGACAGGCTCCAGACAGGTATGAGAGGTGCCTTTGGAAAACCTCAAGGGACTGTTGCCAGGGTCCATATTGGCCAAG
TCATCATGTCCATCCGCACCAAGCTTCAGAACAAGGAGCATGTGATTGAAGCCTTACGCAGGGCAAAATTCAAGTTCCCG
GGACGCCAGAAGATCCATATCTCCAAGAAGTGGGGCTTTACCAAGTTTGATGCTCACGAATTTGAAGACAAAGTGGCCAA
GAAGCGCCTGATTCCTGATGGCTGTGGAGTCAAATACATCCCCAATCGTGGCCCTTTGGACAAGTGGCGGGCCTTGCACT
CCTGA

Alignment

ORF - retro_itri_174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPAPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAA
          MGRRPARCYRYCKNKPYPKSRFCRGV..PDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAA
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRGV--PDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAA

Parental  RICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSI
          RICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSI
Retrocopy RICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSI

Parental  RTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDK
          RTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKF.A.EFED.VA.KRLIPDGCGVKYIPNRGPLDK
Retrocopy RTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFDAHEFEDKVAKKRLIPDGCGVKYIPNRGPLDK

Parental  WRALHS
          WRALHS
Retrocopy WRALHS

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_174 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_174 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174 , retro_itri_506,