RetrogeneDB ID: retro_itri_657

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:13440285..13441040(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD11B2
• Ensembl ID: ENSSTOG00000016446
• Aliases: None
• Description: hydroxysteroid (11-beta) dehydrogenase 2 [Source:HGNC Symbol;Acc:5209]

Sequence

>retro_itri_657
CTCTTGGTTGCCCATATGCTGCTGTAGTTACTGCGTGTAGACCTGTGACTGGGCTGCCAGTTGCTGGCTGCACTGGTGAA
CTGCTGGCCCCACTAGACTGACTATGCCAGAACCTTCTGCCCATGCTGGCCACACTGGCCATGTTGGCTGCTCCCAGTTG
GATTGCTTGTCCTGCCTAGCACGCCTACTGCGTCTGCCACTGGCTTCTTGCCGAGTGCTCATCACTGGCTGTGACTCTGG
TTTTGTCAAGGAGATGGCCAAGCAATTGGACACCAGGGTCTTCACATGCTGGCTACCATGTTAGAGTTCAAGAACCCCAA
TGCCCTAAAGCTGAGTGCCTGCTGTTTCCTTTGCCTAAGGCTATTGCAGATGGACCTCACTAAACTGCACACATTAGCTT
TGCACTGAAGTTCACTAAGTCCCACACCAACAGCAGTGGTGTGTGAGACCTGGTCAATAATGCAGGCTTCAGTGATGTGA
AGCTGTCTCCAATGGCCACATTCTGCAACTGCATGGAGGTGAACTTCTTTGACGCACTGTAGCTGACCAAGGGCCTCCTG
CAGCTCTCACACCACTCAAAGGGTTGCATTGTGACAGTGGGCAGCCCAGCAGGGGACATGCTATATCCATGCTTGGCAGC
CTATGGGACCTCCAAGGCAACCTTGACACTACTCAAGGAAACATTCAGCTGTAAACTTCTTTCCTGGAGGATCAAAGTCA
GTGTCATCCAGCCTGATTTCTTCAAAACAGTCAGT

Alignment

ORF - retro_itri_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.75 %
• Parental protein coverage: 66.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVAARALLQLLRADLRL-GRPLLAALA-LLAALDWLCQRLLPPPAALAVLAAAGWIA-LSRLARPLRLPV
          L..A..LL.LLR.DL.L.G.P.......LLA.LD.LCQ.LLP..A.LA.LAA..WIA.LS.LAR.LRLP.
Retrocopy LLVAHMLL*LLRVDL*L<GLPVAGCTGELLAPLD*LCQNLLPMLATLAMLAAPSWIA<LSCLARLLRLPL

Parental  ATRAVLITGCDSGFGKETAKKLDAMGFT-VLATVLELNSPGALELRACCSPRLRLLQMDLTK-PADIRRA
          A...VLITGCDSGF.KE.AK.LD...FT..LAT.LE...P.AL.L.ACC...LRLLQMDLTK..A.I..A
Retrocopy ASCRVLITGCDSGFVKEMAKQLDTRVFT<MLATMLEFKNPNALKLSACCFLCLRLLQMDLTK<TAHISFA

Parental  LEFTRAHTTSTGLWGLVNNAGFNDIVADVELSPVSTFRTCMEVNFFGALELTKGLLPLLRHSKGRIVTVG
          L.FT..HT.S.G...LVNNAGF.....DV.LSP..TF..CMEVNFF.AL.LTKGLL.L..HSKG.IVTVG
Retrocopy LKFTKSHTNSSGV*DLVNNAGFS----DVKLSPMATFCNCMEVNFFDAL*LTKGLLQLSHHSKGCIVTVG

Parental  SPAGDMPYPCLAAYGTSKAAMALLMDSFSCELLPWGIKVSVIQPGCFKTES
          SPAGDM.YPCLAAYGTSKA...LL...FSC.LL.W.IKVSVIQP..FKT.S
Retrocopy SPAGDMLYPCLAAYGTSKATLTLLKETFSCKLLSWRIKVSVIQPDFFKTVS

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_657 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_657 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000016446	1 retrocopy	retro_itri_657 ,