RetrogeneDB ID: retro_itri_1661

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393615.1:409910..410705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC3
• Ensembl ID: ENSSTOG00000016240
• Aliases: None
• Description: histone deacetylase 3 [Source:HGNC Symbol;Acc:4854]

Sequence

>retro_itri_1661
CTTGATATTGACATCCACCATGAAGATGGCATTTAAGAAGCCTTCTACCTCACTGACTGTAGGGTCATGACTGTGTACTT
CCACAATTATGGAAATTACTTCTTCCCTGGTACAGGTGACATGTATAAATTGGAGCAGAAAGTGGCTGCTACTACTGTCT
CAATGTGCCCTTATAGGATGGCATTGATGATCAGAGTTACAAGCACCTTTTCCAACTGGTCATCAACCAGGTGGTGGACT
TCTACCAAGCCACCTGCATCATGTTCCAATGTGGACAGTGTGAAGCTGACTCTGGGTTGGGATCAACTGGGCTTATTCAA
CTTTAGTATCCAAGGGCATAGGGAATGTGTTGAATATATCAAGAGCTTTAATATCCCTCTACTGGTGCTGGGTGGTGGAG
GCTATACTGTCTAAAACATTGCCTGATGCTGGACATATGAGACATCGATGCTGGTAGAAGAGGTCATTAGTGAGGAGCTT
CCCTATAGAGAATACTTTGAGTAATTTTCCCCTGACTTCACACTCTATCCAGATGTCAGCACCCACAGTGAGAATCAGAA
CTCATGCCAGTATCTGGACCAGATCTGCCAGACAGTCTTTGAAAACCTGAAGATGCTGAACCATGCACCTAATGACCAAA
TTCATGATGTGCCTGTTGAACTCCTGACATATGACAGGATTGATAAGGCTGATGCAGAGGAGAGGGGTCCGAAGGAGAAC
TACAGAAAGCCAGAGGCACTGAGTGAATTCTGTGATGGAGACCATGGCAATGACAAGGAAAGCAAAGTGGAAATT

Alignment

ORF - retro_itri_1661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 61.21 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDIDIHHGDGVQEAFYLTD-RVMTVSFHKYGNYFFPGTGDMYE-VGAESGRYYCLNVPLRDGIDDQSYKH
          .DIDIHH.DG..EAFYLTD.RVMTV.FH.YGNYFFPGTGDMY...GAESG.YYCLNVPL.DGIDDQSYKH
Retrocopy LDIDIHHEDGI*EAFYLTDCRVMTVYFHNYGNYFFPGTGDMYK<IGAESGCYYCLNVPL*DGIDDQSYKH

Parental  LFQPVINQVVDFYQPTCIVLQCG---ADSLGCDRLGCFNL-SIRGHGECVEYVKSFNIPLLVLGGGGYTV
          LFQ.VINQVVDFYQ.TCI..QCG...ADS.G....G...L.SI.GH.ECVEY.KSFNIPLLVLGGGGYTV
Retrocopy LFQLVINQVVDFYQATCIMFQCGQCEADS-GLGSTGLIQL>SIQGHRECVEYIKSFNIPLLVLGGGGYTV

Parental  RNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLN
          .N.A.CWTYETS.LVEE.ISEELPY.EYFE.F.PDFTL.PDVST..ENQNS.QYLDQI.QT.FENLKMLN
Retrocopy *NIA*CWTYETSMLVEEVISEELPYREYFE*FSPDFTLYPDVSTHSENQNSCQYLDQICQTVFENLKMLN

Parental  HAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYDGDHDNDKESDVEI
          HAP..QIHDVP..LLTYDR.D.ADAEERGP.ENY..PEA..EF.DGDH.NDKES.VEI
Retrocopy HAPNDQIHDVPVELLTYDRIDKADAEERGPKENYRKPEALSEFCDGDHGNDKESKVEI

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_1661 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1661 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008662	1 retrocopy	retro_mluc_642,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49,
Procavia capensis	ENSPCAG00000010817	1 retrocopy	retro_pcap_298,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661 ,
Tupaia belangeri	ENSTBEG00000007520	1 retrocopy	retro_tbel_1811,