RetrogeneDB ID: retro_itri_395

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:147265..148187(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025866
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSSTOG00000004108
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_itri_395
GCGGTGTGTTCTAGGTCAATGGCTTCTAAGACTCCAGTTGGATTCATTGGACTGGGCAACATGGGGAATCCAATGGCAAA
AAAACTTCATGAAACATGCTTATCCGCTCATTATTTGTGATGTATTCCCTGATGCATGCAAAGAGTTTCAAGAGGCAGGT
GAACAGGTAGTGTCTTCCCCAGCAGATGTAGCTGAAAAGGCTCACAGGATTATTACAATGCTGCCTACCAGTATCAATGC
TGTAGAAGCTTATTCTGGAACAAACGGAATTCTAAAAAAAGTGAAGAAAGGCTCATTATTAATAGATTCCAGTACTATTG
ATCCTTCAGTTTCAAAAGAATTGGCCAAAGAAGTTGAGAAAATGGGAGCAGTTTTCATGGATGCCCCTGTTTCTGGTGGT
GTGGGAGCTGCTTGGTCTGGGAACCTAATGTTTATGGTAGGAGGAGTCGAAGAGGAATTTGCTGCTGCCCAAGAGCTGCT
GGGGTGCATGGGCTCCAATGTGCTGTTTTGTGGAGCTGTTGGGACCGGGCAGGCTGCAAAGATCTGCGACAACATGCAGT
TAGCTATTAGTATGATTGGAACCGCTGAAGCTATGAATCTTGGAATCAGGTTAGGGCTTGACCCAAAACTATTGGCTAAA
ATCCTAAATATGAGTTCAGGACGGTGTTGGTCAAGCGACACTTATAATCCTGTTCCTGCAGTGATGGATGGAGTTCCCTC
TGCTAATAACTATCAGGGTGGATTTGGAACAACACTCATGGCTAAGGATCTGGGATTGGCACAAGACTCTGCTACCAGCA
CAAAGAGCCCAATCCTTCTGGGCAGTCTAGCCCATCAGATCTACAGAATGATGTGTGCAAAGGGCTATTCCAAAAAAGAC
TTCTCATCTGTGTTCCAGTTTCTACGGGAGGAGGAGAACTTC

Alignment

ORF - retro_itri_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVCSRSMASKTPVGFIGLGNMGNPMAK-NLMKHGYPLIIYDVFPDACKEFQEAGEQVVSSPADVAEKADR
          .VCSRSMASKTPVGFIGLGNMGNPMAK.N.MKH.YPLII.DVFPDACKEFQEAGEQVVSSPADVAEKA.R
Retrocopy AVCSRSMASKTPVGFIGLGNMGNPMAK>NFMKHAYPLIICDVFPDACKEFQEAGEQVVSSPADVAEKAHR

Parental  IITMLPTSINAVEAYSGTNGILKKVKKGSLLIDSSTIDPSVSKELAKEVEKMGAVFMDAPVSGGVGAARS
          IITMLPTSINAVEAYSGTNGILKKVKKGSLLIDSSTIDPSVSKELAKEVEKMGAVFMDAPVSGGVGAA.S
Retrocopy IITMLPTSINAVEAYSGTNGILKKVKKGSLLIDSSTIDPSVSKELAKEVEKMGAVFMDAPVSGGVGAAWS

Parental  GNLTFMVGGVEEEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNMLLAISMIGTAEAMNLGIRLGLDPK
          GNL.FMVGGVEEEFAAAQELLGCMGSNV..CGAVGTGQAAKIC.NM.LAISMIGTAEAMNLGIRLGLDPK
Retrocopy GNLMFMVGGVEEEFAAAQELLGCMGSNVLFCGAVGTGQAAKICDNMQLAISMIGTAEAMNLGIRLGLDPK

Parental  LLAKILNMSSGRCWSSDTYNPVPGVMDGVPSANNYQGGFGTTLMAKDLGLAQDSATSTKSPILLGSLAHQ
          LLAKILNMSSGRCWSSDTYNPVP.VMDGVPSANNYQGGFGTTLMAKDLGLAQDSATSTKSPILLGSLAHQ
Retrocopy LLAKILNMSSGRCWSSDTYNPVPAVMDGVPSANNYQGGFGTTLMAKDLGLAQDSATSTKSPILLGSLAHQ

Parental  IYRMMCAKGYSKKDFSSVFQFLREEENF
          IYRMMCAKGYSKKDFSSVFQFLREEENF
Retrocopy IYRMMCAKGYSKKDFSSVFQFLREEENF

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_395 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_395 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395 ,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,