RetrogeneDB ID: retro_shar_400

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841596.1:1747740..1748756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR2
• Ensembl ID: ENSSHAG00000015678
• Aliases: None
• Description: fragile X mental retardation, autosomal homolog 2 [Source:HGNC Symbol;Acc:4024]

Sequence

>retro_shar_400
TTCTATGTCATAGAATATGCAGCTTGTGATGCAACTACAATAAGATTATGACCCTGGAATGGCTCCGACCTGTCAATCCC
AGTCCTCTGGCTACCAAAGACAGTTTTTTCAAGGTTACCATGGTGATTCCTGAGATTCTGAGAGAAGCCTACTCCAATGA
CAATGTCCATAAAGAGTCCAAGAAGCCTTTAGGAGCCAACTGTATCTTTCCAAACATCACTAACAGTGAGCTCTTTATTC
TGTCAATAACAGAAGCTCCTATAAAACAGGCATCCTTGCTGGGTTATATGCATTTCCGAAGCCTCCGAACCAAACTGCTG
CTCATGTCCTGAAATGAAGAGGCCACCAAACATTTAGAGACAAGCAAGCAGCTAGTAGCAGTATTCCAGGAAGAATTCAC
AGTACAGGAGGACCTAATGGGACTAGCAATTGGGACTCATGGTGCCAATATCCAACAGGCCCAAAAAGTGCCTGAGGTGA
CAGCCATTGAACTGGGTGAGGAAACTTGCACCTTTTGAATTTATGGGGAAATGCTTGAGGCATGCCAGCAGACCTGAAGC
TACCTTGAATTCTCTGAAGACTCTGTCCAAATGCCCTGGAACCTGGTTGGCAAAGTAATTGGGAAGAATGGGAAAGTGAT
CCCATTGTAGATTGTAGATAAATCTGGTGTGTTGAGAGTTCTAGGGGAAGATGATGACAAGAAGAATCCCAAGGACGAGG
GAATGGTTCCTTTCATATTTGTTGGCACCCAGGAAAATATCAGCAATGCACAGGCTCTCCTGGAATATCACCTCTCTTAC
TTGCAGGAGGTAGAACAGCTTCTCTTAGAAAGGCTACAGATTGATGAGCAGCTTCGACAGATTGGACTGGACTTCTGTAG
CCTTGGAAGTGGCCGAGGGAGCAGTGGTGGTAACAAAACTGGCTATGCTACGGATGAAAGCTCTTCCTCTTCCCTCCATG
CTACTAGAACTTATGGGGGTTGTGGCCATGGCCATAGGACAGGAAGTTCTGGCTAC

Alignment

ORF - retro_shar_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FYVIEYAACDAT-YNEIVTLERLRPVNPSPLATKGSFFKVTMAVPEDLREACSNENVHKEFKKALGANCI
          FYVIEYAACDAT.YN.I.TLE.LRPVNPSPLATK.SFFKVTM..PE.LREA.SN.NVHKE.KK.LGANCI
Retrocopy FYVIEYAACDAT<YNKIMTLEWLRPVNPSPLATKDSFFKVTMVIPEILREAYSNDNVHKESKKPLGANCI

Parental  FLNITNSELFILSTTEAPIKRASLLGDMHFRSLRTKLLLMSRNEEATKHLETSKQLAAAFQEEFTVREDL
          F.NITNSELFILS.TEAPIK.ASLLG.MHFRSLRTKLLLMS.NEEATKHLETSKQL.A.FQEEFTV.EDL
Retrocopy FPNITNSELFILSITEAPIKQASLLGYMHFRSLRTKLLLMS*NEEATKHLETSKQLVAVFQEEFTVQEDL

Parental  MGLAIGTHGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSEDSVQVPRNLVGKVIGK
          MGLAIGTHGANIQQA.KVP.VTAIELGEETCTF.IYGE..EAC.Q..SYLEFSEDSVQ.P.NLVGKVIGK
Retrocopy MGLAIGTHGANIQQAQKVPEVTAIELGEETCTF*IYGEMLEACQQT*SYLEFSEDSVQMPWNLVGKVIGK

Parental  NGKVIQE-IVDKSGVVRVRVEGDNDKKNPREEGMVPFIFVGTRENISNAQALLEYHLSYLQEVEQLRLER
          NGKVI...IVDKSGV.RV..E.D.DKKNP..EGMVPFIFVGT.ENISNAQALLEYHLSYLQEVEQL.LER
Retrocopy NGKVIPL*IVDKSGVLRVLGE-DDDKKNPKDEGMVPFIFVGTQENISNAQALLEYHLSYLQEVEQLLLER

Parental  LQIDEQLRQIGLGFRTPGSGRGSSGGDKTGYATDESSSSSLHATRTYGGRGRGRRTGSSGY
          LQIDEQLRQIGL.F...GSGRGSSGG.KTGYATDESSSSSLHATRTYGG.G.G.RTGSSGY
Retrocopy LQIDEQLRQIGLDFCSLGSGRGSSGGNKTGYATDESSSSSLHATRTYGGCGHGHRTGSSGY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_400 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000018613	1 retrocopy	retro_etel_1220,
Monodelphis domestica	ENSMODG00000007179	1 retrocopy	retro_mdom_2009,
Rattus norvegicus	ENSRNOG00000011876	1 retrocopy	retro_rnor_371,
Sarcophilus harrisii	ENSSHAG00000015678	1 retrocopy	retro_shar_400 ,