RetrogeneDB ID: retro_mdom_1311

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:405278050..405279070(+)
• Located in intron of: ENSMODG00000028646

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002772
• Aliases: None
• Description: None

Sequence

>retro_mdom_1311
AAAGGGATCTTTTTAAGCAATGGTGAAAAGTGGAGACAGAGCAGAGGTTTCTCCCTCATGACTCTGAGGAACTTTGGGAT
GGGGAAGAGAACTGTTGAGGAGAGAATCCAGGAAGAAGCCTAGTGTCTGGTGGAGGAGCTCCAGAAAAAAAAAAAAGGGT
CAGTTCTTCAACCCCACCTTCATCCTGGGCTGTGCTCCCTGCAATGTGATCTGCTCCATCCTCTTTAACAATCGCTTCAA
CTATGATGATGAGAAATTTCGGAGATTGATGAGCCTATTAAATGAAAACTATCAGCTCTTAAACACACCATGGATCCAAC
TCTATAATATGTATCCTTCACTAATAAAATGTCTGCCTGGAAGTCATAGAACCATTCATAAAAATAGTGGCAAAATTATG
GTTTTCTTAATGGACCAAGTGAAGAAGCACCAGGAAACCCTAGATCCAAACAACCCCCGGGACTATATTGATGTTTTCCT
CATCAAAATACAACAGGAGAAACTGAATCCAGAGTCTGCATTCAAGTATCAGGAATTGGTGGCCAATGCATCTACTTAGC
TGCTGGTTCAGAAACAACATCCAGCACCCTGAGATATGGGCTTTTACTGCTCATGAAATACCCAAAGATTCAAGCCAAAG
TTCATGAAGAAATTGGCCAAGTCCTTGGCTCAAGTAGAAAACCCTCCATGCAGGACAGAGTCAAGATGCCTTATGTGGAT
GTTGTTGTGCATGAGATACAGAGATATATTCATCTTGTGTCCTTGATTCTTCCACGATTAGCAGCCTATGACATCCACTT
CCAAAAATACTTGATTCCTAAGGGCACAAAAGTATTCCCCTTGCTCTACTCCATCTTGTATGATAGATAAGCATTTCCCA
ATCCATATGAGTGTGACCCAGAGAACTTCTTGGACAAATCTGGAAACTTTCAGAAGAATGACTGCTTTGTAATATTTTCT
TCGGGAAAGTGCCTCTATCTTGGGGAGAGCTTGGCTCAGATGAATTTATTTCTCTTCCTA

Alignment

ORF - retro_mdom_1311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.92 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QGIFLSNGEKWRQNRRFSLMTLRNFGMGKRSIEERVQEEAQYLVEELR-KTKGQFFDP-TFILGCAPCNV
          .GIFLSNGEKWRQ.R.FSLMTLRNFGMGKR..EER.QEEA..LVEEL.....G....P.TFILGCAPCNV
Retrocopy KGIFLSNGEKWRQSRGFSLMTLRNFGMGKRTVEERIQEEA*CLVEELQXXXXGSVLQP>TFILGCAPCNV

Parental  ICSIVFNNRFNYDDEKFLRLMSLLNENFRLLNTPWIQLYNMYPSLIKHLPGSHRTINKNVLEVRNFIMDE
          ICSI.FNNRFNYDDEKF.RLMSLLNEN..LLNTPWIQLYNMYPSLIK.LPGSHRTI.KN......F.MD.
Retrocopy ICSILFNNRFNYDDEKFRRLMSLLNENYQLLNTPWIQLYNMYPSLIKCLPGSHRTIHKNSGKIMVFLMDQ

Parental  VKKHQETLDPNNPRDYIDGFLIKIQQEKLNPQSAFNYQELVANA-INFLAAGTETTSSTLRYGLLLLMKY
          VKKHQETLDPNNPRDYID.FLIKIQQEKLNP.SAF.YQELVANA.I...A....T.SSTLRYGLLLLMKY
Retrocopy VKKHQETLDPNNPRDYIDVFLIKIQQEKLNPESAFKYQELVANA<IYLAAGSETT-SSTLRYGLLLLMKY

Parental  PKIQAKVHEEIDRVLGSSRKSSMQDRVKMPYVDAVVHEIQRYIHLVSLIIPRLAAQDTHFQKYVIPKGTK
          PKIQAKVHEEI..VLGSSRK.SMQDRVKMPYVD.VVHEIQRYIHLVSLI.PRLAA.D.HFQKY.IPKGTK
Retrocopy PKIQAKVHEEIGQVLGSSRKPSMQDRVKMPYVDVVVHEIQRYIHLVSLILPRLAAYDIHFQKYLIPKGTK

Parental  VFPLLYSVLYDRKAFPNPYEFDPENFLDKSGNFQKNDCFVPFSLGKRLCLGESLARMEVFLFL
          VFPLLYS.LYDR.AFPNPYE.DPENFLDKSGNFQKNDCFV.FS.GK.L.LGESLA.M..FLFL
Retrocopy VFPLLYSILYDR*AFPNPYECDPENFLDKSGNFQKNDCFVIFSSGKCLYLGESLAQMNLFLFL

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	0.24 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	97.45 RPM
SRP007412_liver	0.00 RPM	4056.11 RPM
SRP007412_testis	0.00 RPM	12.57 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1311 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1311 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002772	1 retrocopy	retro_mdom_1311 ,