RetrogeneDB ID: retro_mdom_549

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:267858368..267859632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FTO
• Ensembl ID: ENSMODG00000009684
• Aliases: None
• Description: fat mass and obesity associated [Source:HGNC Symbol;Acc:24678]

Sequence

>retro_mdom_549
ATGAAATGAAGTGAAAGCACCTGTGACCCAGAGCAGGAAGCAAAGAAGCAGAAGCTTCTTAAAGAACTTGGAAAAAGATG
ACTTCCTTATCTAAGCCCCAAAGATACTGAATTCCACTAGCTGTGGCAGGAGAATTATTCCAAACTGATTCTCCAAGAAG
CCAGTAGCATCCCATAATTGTTGCATAAGGAAGTTCAGCAAGCCTTCCTCATCTTGCGCAGGCATGGCTGCTTATTCCAG
GATCTAGTCCGAATCAAAGGGAAAAATTTACTCACACCAGTGTCTTACCTTCTTATTGGAAATCCAAGGTACACTTATAA
GTATCTGAATAGCAGACTCTTCACTGTGCCATGGACGATGGAAAGTTCCAACATAAAATATTCCAAAGTTGAAATATTTG
CAGCTTGTAGAGCCTTCTTGAAGCTTAATGACTACTTGCATAAAGATACAATTCAAGTTTTGGACAAACTACACTTCATA
AAATCCAAGGACAGTGAAGACAGTGCAGTCTTTGGCATGGTCCCAGAACTCTCCAAGAACACTTTGAATGTGGGACATGA
TATGGAACTTAAGAAGAGGACAACTTACAATTTGACCTTGTTGAATTACATGGATCCTCAAGAAATGTCTTACTTGAAAG
AAGAACCTTATTTTGGGATGGGAAAAATGGCTGTGAGCTGGCGTCATGATGAGAACCTAGTAGAAAGGTCCACAGTGGCT
GTATACAGTTACAATTATGAAGGCCCGGAAGTTCTTGATGATGGTGAGCTGAGTCCAGAAGGGAGAAACTCCGCTGTCTA
GCATGTTGGTCTGAAGATAGCTTGGGACATAAAGACACCTGGTTTAGCTGTACCCCTCCATCAAGGAGACTGCTGTCATA
TGCTAGACAATCTTAATTCAACCCATCAACACTGTGTTTTGGCCAGTTGGCAACCTCGATTCAGTTCCACCCACAGAGTG
GCTGAGCATTCAATAGGGACTCTGGATTATATTTTTAAGCAATGCCACTTGGCACTTCAGAATGTAAAAGATGACACGGA
GCCCAGAACTGTGCATTTGAGATCCATGGAGTCATCAGTTATCAAGCAGGGGGAAGAAATTCATAATGAGGTAGAATTTG
AATGGGCTGAGACAGTTTTGGTTTCATGGCCATCGCTATAAGAAGAGCACAGATTGGTGGCAGCTACCCATGTCTGAACT
GGAAGGATTGTGGAAAAAGATGGAATGTGTGACAAATGCAGTGCTTGGTGAATTCAGAACAGAG

Alignment

ORF - retro_mdom_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 89.01 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKRRESTCDPEREAKKQKLLKELGNRWLPYLTPKDTEFHQLWQENYSKLILREASSIPELLHKEVQQAFL
          MK..ESTCDPE.EAKKQKLLKELG.R.LPYL.PKDTEFH.LWQENYSKLIL.EASSIP.LLHKEVQQAFL
Retrocopy MK*SESTCDPEQEAKKQKLLKELGKR*LPYLSPKDTEFH*LWQENYSKLILQEASSIP*LLHKEVQQAFL

Parental  ILRKHGCLFQDLVRIKGKNLLTPVSRLLIGNPGYTYKYLNSRLFTVPWPMEGSNIKYSKDEIFAACRAFF
          ILR.HGCLFQDLVRIKGKNLLTPVS.LLIGNP.YTYKYLNSRLFTVPW.ME.SNIKYSK.EIFAACRAF.
Retrocopy ILRRHGCLFQDLVRIKGKNLLTPVSYLLIGNPRYTYKYLNSRLFTVPWTMESSNIKYSKVEIFAACRAFL

Parental  KLNDYLRKDTIQALDKLHLIKSKDSEDSAVFGMVPELSKNILNVGHDMELKKRTTYNLTLLNYMDPQEMS
          KLNDYL.KDTIQ.LDKLH.IKSKDSEDSAVFGMVPELSKN.LNVGHDMELKKRTTYNLTLLNYMDPQEMS
Retrocopy KLNDYLHKDTIQVLDKLHFIKSKDSEDSAVFGMVPELSKNTLNVGHDMELKKRTTYNLTLLNYMDPQEMS

Parental  YLKEEPYFGMGKMAVSWHHDENLVERSTVAVYSYNCEGPEVLDDDELSPEGRNPAVWHVGLKIAWDIKTP
          YLKEEPYFGMGKMAVSW.HDENLVERSTVAVYSYN.EGPEVLDD.ELSPEGRN.AV.HVGLKIAWDIKTP
Retrocopy YLKEEPYFGMGKMAVSWRHDENLVERSTVAVYSYNYEGPEVLDDGELSPEGRNSAV*HVGLKIAWDIKTP

Parental  GLAVPLHQGDCYLMLDNLNSTHQHCVLAGLQPRFSSTHRVAECSAGTLDYIFKQCHLALQNVKDDTEPRT
          GLAVPLHQGDC..MLDNLNSTHQHCVLA..QPRFSSTHRVAE.S.GTLDYIFKQCHLALQNVKDDTEPRT
Retrocopy GLAVPLHQGDCCHMLDNLNSTHQHCVLASWQPRFSSTHRVAEHSIGTLDYIFKQCHLALQNVKDDTEPRT

Parental  VHLRSMESSVIKQGEEIHNEVEFEW-LRQFWFHGHRYKKCTDWWQLPMSELEGLWKKMECVTNAVLDEIR
          VHLRSMESSVIKQGEEIHNEVEFEW.LRQFWFHGHRYKK.TDWWQLPMSELEGLWKKMECVTNAVL.E.R
Retrocopy VHLRSMESSVIKQGEEIHNEVEFEW>LRQFWFHGHRYKKSTDWWQLPMSELEGLWKKMECVTNAVLGEFR

Parental  KE
          .E
Retrocopy TE

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	13.83 RPM
SRP007412_cerebellum	0.00 RPM	16.65 RPM
SRP007412_heart	0.00 RPM	14.75 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	7.55 RPM
SRP007412_testis	0.00 RPM	31.43 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_549 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_549 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009684	1 retrocopy	retro_mdom_549 ,