RetrogeneDB ID: retro_itri_618

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393306.1:266297..266855(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS2
• Ensembl ID: ENSSTOG00000006207
• Aliases: None
• Description: HAUS augmin-like complex, subunit 2 [Source:HGNC Symbol;Acc:25530]

Sequence

>retro_itri_618
ATGGCTGCGGCCAACCCTGGGGACCCGGCTTCCACGCCAAACTCCGCAGGGCTACTGTTGCGCCACTTCGTGGCTTCAGG
GTTGGTCACTCAGGAGATGTTAAATATATCTACGAAAGCAGCTCCTTGCTTTGAGAAATTCCCCAGACTACAACAGATCA
CAAATATTCAAGCCGAAATCTATCAGAAAAGCCTGGAAATTGAACTTCTGAAACTAGAAAAAGATGCAGCAGATGTTGTT
CATCCTTTCTCTTTGTCTCAAAAGTGTCATGATCTACAAAGTATGAATAATCACCTGGAAGCTGTGCTGAAAGGAAAGAG
GTCCCTCAGGCAAAGACTGTTGAGACCCATGTGCCAGGAAAACTTACCTTTGGAGGCTTTTTATCACAGATATGTGGTAC
ATTTGCTGGAGTTGGCTGTGACTTTCATTGAGAGATTGGAAACCCATCTTTAAACAATTAGAAATATCCCTCATTTGGAT
GCAAATCTAAAGAAAAGGAGCAAGGCTTTAACCAAGATGGATGTTTTGGTGACTGAGACAGAAGAACTGGCAGAGAAT

Alignment

ORF - retro_itri_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 79.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAANAWDPASAPNSAGLLLGHFVASGLVTQEMLNISKRTAPCFEKFSRLQQITNIQAEIYQKSLEIELL
          MAAAN..DPAS.PNSAGLLL.HFVASGLVTQEMLNIS...APCFEKF.RLQQITNIQAEIYQKSLEIELL
Retrocopy MAAANPGDPASTPNSAGLLLRHFVASGLVTQEMLNISTKAAPCFEKFPRLQQITNIQAEIYQKSLEIELL

Parental  KLEKDAADVVHPFYLSQKCHDLQSMNNHLEAVLKEKRSLRQRLLKPMCQENLPLEAFYHRYMVHLLELAV
          KLEKDAADVVHPF.LSQKCHDLQSMNNHLEAVLK.KRSLRQRLL.PMCQENLPLEAFYHRY.VHLLELAV
Retrocopy KLEKDAADVVHPFSLSQKCHDLQSMNNHLEAVLKGKRSLRQRLLRPMCQENLPLEAFYHRYVVHLLELAV

Parental  CFIERLETHLETIRNIPHLDANLKKMSKALTKMDVLVTETEELAEN
          .FIERLETHL.TIRNIPHLDANLKK.SKALTKMDVLVTETEELAEN
Retrocopy TFIERLETHL*TIRNIPHLDANLKKRSKALTKMDVLVTETEELAEN

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_618 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_618 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003587	4 retrocopies	retro_meug_1171, retro_meug_1231, retro_meug_702, retro_meug_996,
Microcebus murinus	ENSMICG00000000819	1 retrocopy	retro_mmur_648,
Monodelphis domestica	ENSMODG00000017882	1 retrocopy	retro_mdom_1473,
Oryctolagus cuniculus	ENSOCUG00000011004	1 retrocopy	retro_ocun_1322,
Sorex araneus	ENSSARG00000001275	2 retrocopies	retro_sara_123, retro_sara_413,
Ictidomys tridecemlineatus	ENSSTOG00000006207	1 retrocopy	retro_itri_618 ,
Vicugna pacos	ENSVPAG00000006260	1 retrocopy	retro_vpac_599,