RetrogeneDB ID: retro_mdom_2009

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:15471858..15473193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR2
• Ensembl ID: ENSMODG00000007179
• Aliases: None
• Description: fragile X mental retardation, autosomal homolog 2 [Source:HGNC Symbol;Acc:4024]

Sequence

>retro_mdom_2009
CGGCTAGCAGCTGCATTCCAAGACGAATTTACAGTACAGGAAGACCTAATGGGATTAGCAATTGGAACTCTTGGTGCCAA
TATTCAGTAGGCCCAAAAAGTGCCTGGGGTGACAGTCATTGAACTGGTCGAGGAGACTTGCACCTTCTGAATCTACAGGA
AGACCCCTGAAGCATGCCGGTAGGCCCAAATCTACCTAGAGTTTTCCGAAGACTCTGTCCAAGTGCCCTGGAACCTGGTT
GGAAAAGAGATTAAGAAGAATGGGAAAGTGATCCAGGAGATTGTGGATAAATCTGGTGTGGTGAGGTTTCGAGTGGAGGG
TGGTAATGACAAGAAGAATCCAAGGGAGGAGGGAATGGTTCCTTTCACATTTGTTGGTACCTGGGAGAACATCAGCAATG
CTCAGGCCCTACTGGAATATCACCTCTCTTACTTGCAGCAAGTAGAACAGTTTCAATTAGAAAGACTACTGATTGATGAA
CAACTTCAGCAGATTGGGCTGGGCTTCTGTACCCCTGGAACTGATCGAGGAAACAGTAGTGGTGACAAGACTGGCTACGC
CACAGATGAAAGCTCTTCCTCTTCCCTCCATGCCACTAGTTCCTATGGGGATTGTGGCCATGGCCGGAAGACAGGAAGTT
CTGGCTATGGCCCTGGTTCAGATCGGTCCACTGCTTCTGAAACTGAGTCTGAGAAACAAGAGGAGCCTGACCAGTCTGCA
CATGGTGAGCAGGGTTCCTCTAGACTTGGTGAAAAGGATCGTAGGAGACCAATGGGGGTCCGAGGTCGAGGGTCTAATCC
TAAACCTCGGCTTCCTAGCAAGGATACAACACCTTCCATTATCTCAGTGCTGAAGGATCCTGACAGTAATCCCTACTGCC
TACTGGACACATCAGAACCAGAGCCCCCAGTTGACTCTGAGCCTGAAGAGCCACCTCCAGCTATTGCCCATCAACGACAT
TCCCTCCATCACCATAGAGATGAGGATCGGACCATCATAGATGGAGGACTGGAATCTGATGGCCCTAATCTGGCTGAAAA
TGGTCTGGAAGAATAATCAAAACCCCAATGACTCAACAGAAGCCATAGATGACATAAATGTGGTAACCAAGCAGATGACT
CCATCAGCAGAGATCGGCAGCCAGTGACAGTGGCAGATTACATCTCCTAGGCAGAATCTCAGAGCCGACAGAGGCAGCCC
CCTGATCCCACTCATGTTCCTTCCGAGGACTCTCTCTCAAGACCAAAGGGTGTCAGCAAGCTTTCTAAGGGCCCCTCGGA
AAATGGAGAGTTCTCTGCCTCCTTGGAGCTGGGCAGCTTGGTGAATGGGATCTCA

Alignment

ORF - retro_mdom_2009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.25 %
• Parental protein coverage: 77.66 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLAAAFQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSE
          .LAAAFQ.EFTV.EDLMGLAIGT.GANIQ.A.KVPGVT.IEL.EETCTF.IY..TPEACR.A..YLEFSE
Retrocopy RLAAAFQDEFTVQEDLMGLAIGTLGANIQ*AQKVPGVTVIELVEETCTF*IYRKTPEACR*AQIYLEFSE

Parental  DSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREEGMVPFIFVGTRENISNAQALLEY
          DSVQVP.NLVGK.I.KNGKVIQEIVDKSGVVR.RVEG.NDKKNPREEGMVPF.FVGT.ENISNAQALLEY
Retrocopy DSVQVPWNLVGKEIKKNGKVIQEIVDKSGVVRFRVEGGNDKKNPREEGMVPFTFVGTWENISNAQALLEY

Parental  HLSYLQEVEQLRLERLQIDEQLRQIGLGFRTPGSGRGNSSGDKTGYATDESSSSSLHATRTYGGRGRGRR
          HLSYLQ.VEQ..LERL.IDEQL.QIGLGF.TPG..RGNSSGDKTGYATDESSSSSLHAT..YG..G.GR.
Retrocopy HLSYLQQVEQFQLERLLIDEQLQQIGLGFCTPGTDRGNSSGDKTGYATDESSSSSLHATSSYGDCGHGRK

Parental  TGSSGYGPGSDLSTASETESEKREEPDRPGHGDQDTSSRGEEGRRRPMGGRGRGSNPAPRLPSKYTTSSI
          TGSSGYGPGSD.STASETESEK.EEPD...HG.Q..S..GE..RRRPMG.RGRGSNP.PRLPSK.TT.SI
Retrocopy TGSSGYGPGSDRSTASETESEKQEEPDQSAHGEQGSSRLGEKDRRRPMGVRGRGSNPKPRLPSKDTTPSI

Parental  SSVLKDPDSNPYSLLDTSEPEPPVDSEPGEPPPASARRRRSRRRRTDEDRTIIDGGLESDGPNLAENGLE
          .SVLKDPDSNPY.LLDTSEPEPPVDSEP.EPPPA.A..R.S.....DEDRTIIDGGLESDGPNLAENGLE
Retrocopy ISVLKDPDSNPYCLLDTSEPEPPVDSEPEEPPPAIAHQRHSLHHHRDEDRTIIDGGLESDGPNLAENGLE

Parental  EESKPQRRNRSRRRRNRGNRADGSISRDRQPVTVADYISRAESQSRQRQPPEPTHVPSEDSLSGPKGVSK
          E.SKPQ..NRS.R....GN.AD.SISRDRQPVTVADYIS.AESQSRQRQPP.PTHVPSEDSLS.PKGVSK
Retrocopy E*SKPQ*LNRSHR*HKCGNQADDSISRDRQPVTVADYIS*AESQSRQRQPPDPTHVPSEDSLSRPKGVSK

Parental  LPKGPSENGELSASLELGSLVNGVS
          L.KGPSENGE.SASLELGSLVNG.S
Retrocopy LSKGPSENGEFSASLELGSLVNGIS

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2009 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2009 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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,