RetrogeneDB ID: retro_itri_681

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:8819179..8819849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSSTOG00000001593
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit [Source:HGNC Symbol;Acc:4801]

Sequence

>retro_itri_681
ATAGTGACCTCCTGGGCAATTGGCAGCCTTAGACACTTCAATGCCTTCAAGATATTCTGCTCCCGAGGTTGTATTTGCTG
CAACTTTTCAGGGTCTTCTGCTTTGCTAGAACCCATGTTAATTTGGGGCTCAAAGAGAATGTGACAGTTATTTGCACTAA
TTCACCCAGTTCAAAGGTAAATACACTGAATGAAGAAGTACAATCAGAATTCATGGAAATGATCAAATCAGGGCCAGTGA
TCAAATCTAAAGTGCCAACCTCATCTCATCAAAGCCAGTTTTGTTTTCTTGCAGGTGCTGATATCAACATGTCAGCCTCT
TGTAGACTCTGCAAGAAGTAACACAAATACCAAAGGAAGGATAGAGAATGTTTGAGAAACTTAGAAAGTTCCCAAAATCT
GTTGTAGCTGCCATCAGTGGATCTTGCTTGGAAGGAGGACTTGAGTTTGTCATTGTATGCCAATACAGAATAGCAACAAA
AGATAGGAAAACAGTATTAGTCATCCCTGAATTCTTGCTGGGGATCCTACCAGGAGAGGGAGACACCTAAAGCCCGCCCA
AAATGGTGGGTGCACCTGCTGCTTTTATCATGATGCTGACAGGTAGAAACATTCACACAGGCGGAGCAAAGAAAATGAGA
CTGGTTGGTCAACTGGAGGGAACCCTCGGG

Alignment

ORF - retro_itri_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.52 %
• Parental protein coverage: 84.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVASRAIGSLNRFNAFRILRSRGCSCRNFSGSSALL-ARTHVNYGVKGNVAVIRLNSPNSKVNTLNKEVQ
          .V.S.AIGSL..FNAF.I..SRGC.C.NFSG.S..L.ARTHVN.G.K.NV.VI..NSP.SKVNTLN.EVQ
Retrocopy IVTSWAIGSLRHFNAFKIFCSRGCICCNFSG-SSAL<ARTHVNLGLKENVTVICTNSPSSKVNTLNEEVQ

Parental  TEFMEVMDEIWASDQIKSAVLISSKPG--CFVAGADINMLASCK-TPQEATQISQEGQRMFEKLERSPKP
          .EFME....I.....IKS.V..SS.....CF.AGADINM.ASC..T.QE.TQI..EG.RMFEKL...PK.
Retrocopy SEFMEM---IKSGPVIKSKVPTSSHQSQFCFLAGADINMSASCR<TLQEVTQIPKEG*RMFEKLRKFPKS

Parental  VVAAINGSCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRN
          VVAAI.GSCL.GGLE..I.CQYRIATKDRKTVL..PE.LLGILPG.G.T...PKMVG.PAAF.MMLTGRN
Retrocopy VVAAISGSCLEGGLEFVIVCQYRIATKDRKTVLVIPEFLLGILPGEGDT*SPPKMVGAPAAFIMMLTGRN

Parental  IRADRAKKMGLVDQLVEPLG
          I....AKKM.LV.QL...LG
Retrocopy IHTGGAKKMRLVGQLEGTLG

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_681 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_681 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681 ,