RetrogeneDB ID: retro_itri_374

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393287.1:10008130..10009183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSSTOG00000012779
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_itri_374
TCAAGTGCCGTGAAACTAAATAAGCAGCAGAGGGACATTGCTGTGAATTGGGCTGGGGGCCTGCACCATGCAAAGAAGCC
CGAGGCATCAGGCTTCTGTTACATCGATGATATCGTCTTGGCCATCCTGGAACTGCTGAAGTATCACCCGAGGGTGCTAT
AATTGACATTGATGTTCACCATGGCCATGGTGGGGAAGAGCCCTTCTATACCACAGGAGGAGTCGAGACTGTGTCCTTTC
ATAAATATGGAGAGTACTTCCCAGGAACTGGAGACCTACAGGAACTGGCAAAGGCAAGTATCGTGCTGTTAACTACCCAC
TCCGAGATGGGATTGATGACAAGTCCTCTGAGGCCATTTTCAAGCTGGTCATGTCCAAAGTATTGGAGATGTTCCAGCCT
AGCGTGGTGGTCTTACAATGTGGCTCAGATTCCCTGTCTGGGCATCAGGTCGGTTGCTTCAATCTGACCACCAAAGGGCA
TGCCAAGTGGGTAGAATTTGTGAAGAGCTTCAACCTGCCTATGCTGTTGCTGGGAGGAGGTGGTCACACCATTCGTAATG
TGGCCCGGTGCTGGACATACGAAACGGCTGTGGCTCTGGACACAGATTCCCCAATGAGCTTCCATACAATGACTACTTCG
AGTACTTTGGACCCGATTTCAAGCTTCACATCAGTCCTTCCAATATGACTGATCAGAACATGAAGGAGGACCTGGAGAAG
ATAAAACAGCGGCTCTTTGAGAACCTGAGAATGCTGCCCCGTGCACCTGAAATCCAGTCCATTCCCGAGGATGCCATCCC
AGAGGAGAGTGGTGATGAGGATGAAGAAGACCCTGACAAGCGTATCTCCATCTGTTCCTCTGACAACTGAACTGCCTGTG
AGGAAGAATTCTCTGACTCAGATGAGGAAGGAGAGGGGGGCCACAAAAACTCTTCCGGCTTCAAAAAAGCCAAGGGAGTC
AAAACAGAGAAAGACCCAGAGGAGAAGGAAGAAGTCACAGAAGAGGAGAGAACCAAGGAGGAGAAGCCAGAAGCCAAAGG
GGTCAAACAGGAG

Alignment

ORF - retro_itri_374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.3 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVL-YIDIDIHHGDGVEEAF
          ..AVKLN.QQ.D.AVNWAGGLHHAKK.EASGFCY..DIVLAILELLKYH.RVL..IDID.HHG.G.EE.F
Retrocopy SSAVKLNKQQRDIAVNWAGGLHHAKKPEASGFCYIDDIVLAILELLKYHPRVL<IIDIDVHHGHGGEEPF

Parental  YTTDRVMTVSFHKYGEYFPGTGDLRDI-GAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSA
          YTT..V.TVSFHKYGEYFPGTGDL....G.G..KY.AVN.P.RDGIDD.S...IFK...SKV.EM.QPS.
Retrocopy YTTGGVETVSFHKYGEYFPGTGDLQEL<GKG--KYRAVNYPLRDGIDDKSSEAIFKLVMSKVLEMFQPSV

Parental  VVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCE-IP
          VVLQCG.DSLSG...GCFNLT.KGHAK.VE.VK.FNLP.L.LGGGG.TIRNVARCWTYETAVALD....P
Retrocopy VVLQCGSDSLSGHQVGCFNLTTKGHAKWVEFVKSFNLPMLLLGGGGHTIRNVARCWTYETAVALDTD<FP

Parental  NELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGD
          NELPYNDYFEYFGPDFKLHISPSNMT.QN..E..EKIKQRLFENLRMLP.AP....Q.IPEDA..E.SGD
Retrocopy NELPYNDYFEYFGPDFKLHISPSNMTDQNMKEDLEKIKQRLFENLRMLPRAP--EIQSIPEDAIPEESGD

Parental  EDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKADVKEEDK
          ED.EDPDKRISI..SD...AC.EEFSDS..EGEGG..N....KK.AK....E.D..E.E.....V.EE..
Retrocopy EDEEDPDKRISICSSDN*TACEEEFSDSDEEGEGGHKNSSGFKK-AKGVKTEKDPEEKEE----VTEEER

Parental  SKDNSGEKTDTKGAKSE
          .K....EK...KG.K.E
Retrocopy TKE---EKPEAKGVKQE

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_374 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_374 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374 ,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,