RetrogeneDB ID: retro_mdom_92

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:272787890..272789618(+)
• Located in intron of: ENSMODG00000021457

Retrocopy information

• Ensembl ID: ENSMODG00000024723
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009731
• Aliases: None
• Description: Alpha-(1,6)-fucosyltransferase [Source:UniProtKB/TrEMBL;Acc:F6XAH5]

Sequence

>retro_mdom_92
ATGAGGCCATGGTTTGGCTCCTGGCGTTGGATTATGCTCATTCTCTTTGCTTGGGGGACCTTGCTCTTTTATAGAGGTGG
ACACCTGGTAGGGGACAATGACCATCCTGATCACTATAGACAAGAAATCTCCAAGATACTGTCAAAGCTTGAACACTTAA
AACAACAGAATGAAAACTTGAGGCGGATGGCAGAGTTTCTCAGGATACCAGAAGATCCCATGGACCAGGGACCAGATTCA
GGAAGGGTACGTACTTTAAAAGAACAGTTTTTAAAAGGCAAAGAACAGATAGAAAATTACAAGAAGAAAACCAGAGATGT
AGGTCTAGGGAAGAATTATGAAATACTGAGGAAGATTGAAAATGGAGCTAAGGAGCTTTGGTTTTTTCTCCAGAGTGAAC
TGAAGAAATTGAAAGATTTAGAAGGAATTGACCTCCAAAGACATGTGGATGAATTTCTATTTGATTTGGGTCATCAGGAA
AGGTCAATAATGACAGATCTGTACTACCTCAGTCAAGCAGATGGAGCTGGTTATTGGAGAGAAAAAGAAGCCAAAAACCT
GACAGAACTAGTCCAAAGGAGAATAACATATCTTCAGAACCCCAAGAATTGCGAAAAAGCCAAGAAACTGGTATGTAATA
TCAACAAAAATTGTGGCTATGGCTGTCAACTCCACCATGTTGTCTACTGCTTCATGATTGCATATGGCACTCAAAGAACT
CTCATTCTGGAATCCCATAAGTGGCACTATGCTACTGGTGGATGGGAGACTGTATTTAGACCTTTAAGTGAGACATGCAC
AAACAGAGAAGGCAGCACTAATAGACTCTGGTCAGGTGAGATAAATGACAAAAATATTCAAGTAGTAGACCTTCCCATTG
TTGACTTCCTTCATCCACGGCCACCTTATTTACCACTGGCTATTCCAGAAGACCTTGCAGATCGACTAGTGCGGATCCAT
GGAGATCCCGCCGTGTGGTGGGTTTCCCAGTTTGTCAAATACTTAATCCGTCCACAGCCTTGGTTAAAAAAGAAAATTGA
AGAAGCCACCAAAAAGCTTGGTTTCAAGCACCCAGTTATCGGAGTTCATGTTCGACGTACAGACAAAGTGAGAACAGAAG
CCGCATTCCATTCCATTGAGGAATACATGGTTCATGTTGAAGAGCATTTCCAGCTTCTTGAATGCAGAATACATGTGGAC
AAAAAAAGAGTTTATCTGGCCACAGATGATCCTTCCTTATTGAAACAGGCAAAGGCCAAGTACCCAAATTATGAATTTAT
CAGTAATAACTCCATATCCTGGTTAGCTGGACTAGGTAATCGATATACATTCAATTCCCTACAAGGTGTAATTTTGGATA
TACACTTTCTGTCACAAGCAGATTTCCTAGTCTGTACGTTTTCATCTCATGTTTGTCGAGCTGCTTATGAAATCATGCAG
ACACTACATCCTGATGCCTCTGCCTACTTCCATTCTTTGGATGACATTTACTATTTTGGGGGCCAGAATGCCCACAACCA
GATTGCTATTTATCCTCACCGACCACGAACTGCTAATGAAATCCCTATGGATCCTGGAGATGTCATTAGCGTGATCGGAA
ACCACTGGGATGGCTATTCTAAAGGTTTCAATGAGAATCAAGGGAGAATAGGCTTGTACCCTTCCTATAAAGTGAAAGAA
AAAATAGAGACAGTCAAGTACCCCACATACCCAGAAGCTGAGAAATAA

Alignment

ORF - retro_mdom_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPWTGSWRWIMLILFAWGTLLFYIGGHLVRDNDHPDHSSRELSKILAKLERLKQQNEDLRRMAESLRIP
          MRPW.GSWRWIMLILFAWGTLLFY.GGHLV.DNDHPDH...E.SKIL.KLE.LKQQNE.LRRMAE.LRIP
Retrocopy MRPWFGSWRWIMLILFAWGTLLFYRGGHLVGDNDHPDHYRQEISKILSKLEHLKQQNENLRRMAEFLRIP

Parental  EGPMDQGPATGRVRALEEQLLKAKEQIENYKKQTRDAGLGKDHEILRRRIENGAKELWFFLQSELKKLKN
          E.PMDQGP..GRVR.L.EQ.LK.KEQIENYKK.TRD.GLGK..EILR..IENGAKELWFFLQSELKKLK.
Retrocopy EDPMDQGPDSGRVRTLKEQFLKGKEQIENYKKKTRDVGLGKNYEILRK-IENGAKELWFFLQSELKKLKD

Parental  LEGSDLQRHVDEFLFDLGHQERSIMTDLYYLSQADGAGDWREKEAKGLTELVQRRITYLQNPKDCRKAKK
          LEG.DLQRHVDEFLFDLGHQERSIMTDLYYLSQADGAG.WREKEAK.LTELVQRRITYLQNPK.C.KAKK
Retrocopy LEGIDLQRHVDEFLFDLGHQERSIMTDLYYLSQADGAGYWREKEAKNLTELVQRRITYLQNPKNCEKAKK

Parental  LVCNINKGCGYGCQLHHVVYCFMIAYGTQRTLILESHNWRYATGGWETVFRPVSETCTDRAGSTTGHWSG
          LVCNINK.CGYGCQLHHVVYCFMIAYGTQRTLILESH.W.YATGGWETVFRP.SETCT.R.GST...WSG
Retrocopy LVCNINKNCGYGCQLHHVVYCFMIAYGTQRTLILESHKWHYATGGWETVFRPLSETCTNREGSTNRLWSG

Parental  EINDKNIQVVELPIVDSLHPRPPYLPLAVPEDLADRLVRIHGDPAVWWVSQFVKYLIRPQPWLEKEIEEA
          EINDKNIQVV.LPIVD.LHPRPPYLPLA.PEDLADRLVRIHGDPAVWWVSQFVKYLIRPQPWL.K.IEEA
Retrocopy EINDKNIQVVDLPIVDFLHPRPPYLPLAIPEDLADRLVRIHGDPAVWWVSQFVKYLIRPQPWLKKKIEEA

Parental  TKKLGFKHPVIGVHVRRTDKVGTEAAFHPIEEYMVHVEEHFQLLERRIHVDKKRVYLATDDPSLLKEAKS
          TKKLGFKHPVIGVHVRRTDKV.TEAAFH.IEEYMVHVEEHFQLLE.RIHVDKKRVYLATDDPSLLK.AK.
Retrocopy TKKLGFKHPVIGVHVRRTDKVRTEAAFHSIEEYMVHVEEHFQLLECRIHVDKKRVYLATDDPSLLKQAKA

Parental  KYPNYEFISDNSISWSAGLHNRYTENSLRGVILDIHFLSQADFLVCTFSSQVCRVAYEIMQTLHPDASAY
          KYPNYEFIS.NSISW.AGL.NRYT.NSL.GVILDIHFLSQADFLVCTFSS.VCR.AYEIMQTLHPDASAY
Retrocopy KYPNYEFISNNSISWLAGLGNRYTFNSLQGVILDIHFLSQADFLVCTFSSHVCRAAYEIMQTLHPDASAY

Parental  FHSLDDIYYFGGQNAHNQIAVYPHRPRTADEIPMDPGDVIGVAGNHWDGYSKGVNRKLGRTGLYPSYKVK
          FHSLDDIYYFGGQNAHNQIA.YPHRPRTA.EIPMDPGDVI.V.GNHWDGYSKG.N...GR.GLYPSYKVK
Retrocopy FHSLDDIYYFGGQNAHNQIAIYPHRPRTANEIPMDPGDVISVIGNHWDGYSKGFNENQGRIGLYPSYKVK

Parental  EKIETVKYPTYPEAEK
          EKIETVKYPTYPEAEK
Retrocopy EKIETVKYPTYPEAEK

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	153.41 RPM
SRP007412_cerebellum	0.00 RPM	360.08 RPM
SRP007412_heart	0.00 RPM	26.12 RPM
SRP007412_kidney	0.00 RPM	56.62 RPM
SRP007412_liver	0.00 RPM	9.06 RPM
SRP007412_testis	0.00 RPM	98.41 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_92 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_92 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010918	1 retrocopy	retro_etel_33,
Monodelphis domestica	ENSMODG00000009731	1 retrocopy	retro_mdom_92 ,
Tarsius syrichta	ENSTSYG00000000574	1 retrocopy	retro_tsyr_1683,