RetrogeneDB ID: retro_mdom_1932

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:185219225..185220307(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXW5
• Ensembl ID: ENSMODG00000017319
• Aliases: None
• Description: F-box and WD repeat domain containing 5 [Source:HGNC Symbol;Acc:13613]

Sequence

>retro_mdom_1932
GAACTGGCCATCTCACTCCTACAAAGCTCCAACATGAGGCCTTATAACTGGAGCTACACTCAGTTTTCCCAGTTTCCAAC
AGGATGACACACTGCTTCTCATGTCAGGAGTCTTCCTAAGGCCCCATAACTCTTCATCAGGAGAGATTGCTGTCATCAGC
TTGGATAACTTTGCTCTCCTCTCATGGGTGCGAAACAAGCCATATGATATGTTTGGATGCGGGCTAAATGAAACCAATCT
GATCATTGGGAATCTACACCGAATTGGAGATATGACATCCTGCTCTGTGCTCTGGCTCAACAATGCCTTTCAGGATGTCG
TGTCAGAGAATGCTAATGTGGTGAAGTGGCTCTTCAAAATCCAGAACTTTAATGCTAGTACTATCTGTACTGTGATGGTG
GCTGACTGCAGTCACTATGATAGCCCTGACCTCTTCCTCGATGCTGGAACCCAGCTAACTTCTGCCACCACCTTTCCTTG
CTGGGTTTTTAACCTGGGTAGTGATGAGGAAGAGGAAAGCTGGAACTGACCCCCATTAGAAGCCCAGCCAAGGGGTGGGT
GGGTGGAGGAGCAATGAGGGACTTCGGTACTTCCTAGATGATATCATGGAGGGGCAGGCATGACCTTTCTTGTCAGAGCA
GGAATTGGAGAGCAAAGGTGAAGAGTTTCTGGCCCAGATTCAGACCAAAGCCCCTGAGACAAGCAGAGAAGGTAGCGACA
AGAAGAAATATTTGATCTTCACTATTGGCTGCCTCACCTACTTCCCACACCAGATAGGGATTAAACAGATCCTTCCTCAC
CAGATGACAACTACAGGGCCAGTACTGGGAGAAGAGGGGCATTCAGATGAGTTTTTTGACTCATTGGATCACATGATTGA
CATCCATGGACACATCATTGGAATGGGACTGTCACCTGACCACAGGTACCTATATGTCAACAGCTGCTCATGGCCCAGTG
GCTCAGTGGTGTTAGACCCTATGCAGCCACCACCTATTGCTGAGGAGATTGACTTACATGTGTTTGACCTTAAGACTATG
AAGGAAGTAAAGAGGGCCCTCAGAGCCCACTGTGTTGTGACA

Alignment

ORF - retro_mdom_1932 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.01 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLAISLLHSSNMRPYNWSYTQFSQF-NQDDTLLLVSGVFLGPHNSSSGEIAVISLDNFALLSRVRNKPYD
          .LAISLL.SSNMRPYNWSYTQFSQF..QDDTLLL.SGVFL.PHNSSSGEIAVISLDNFALLS.VRNKPYD
Retrocopy ELAISLLQSSNMRPYNWSYTQFSQF>QQDDTLLLMSGVFLRPHNSSSGEIAVISLDNFALLSWVRNKPYD

Parental  VFGCWLNETNLISGNLHRIGDITSCSVLWLNNAFQDVESENVNVVKRLFKIQNLNASTIRTVMVADCSRY
          .FGC.LNETNLI.GNLHRIGD.TSCSVLWLNNAFQDV.SEN.NVVK.LFKIQN.NASTI.TVMVADCS.Y
Retrocopy MFGCGLNETNLIIGNLHRIGDMTSCSVLWLNNAFQDVVSENANVVKWLFKIQNFNASTICTVMVADCSHY

Parental  DSPDLLLDAGPQLTSVTTSPCRVFDLGSDNEEEE-SWNPPPLEAQSRGG--PKEGLRRFLDDIMEWRARP
          DSPDL.LDAG.QLTS.TT.PC.VF.LGSD.EEE.....P.....Q..GG....EGLR.FLDDIME..A.P
Retrocopy DSPDLFLDAGTQLTSATTFPCWVFNLGSDEEEES>GTDPH*KPSQGVGGWRSNEGLRYFLDDIMEGQA*P

Parental  VLSEQELESKVAEFLAQSRTKAPETSRESSDKKKYLIFTTGCLTYSPHQIGIKQILPHQMTTAGPVLGEE
          .LSEQELESK..EFLAQ..TKAPETSRE.SDKKKYLIFT.GCLTY.PHQIGIKQILPHQMTT.GPVLGEE
Retrocopy FLSEQELESKGEEFLAQIQTKAPETSREGSDKKKYLIFTIGCLTYFPHQIGIKQILPHQMTTTGPVLGEE

Parental  RRSDEFFDSLDHVIDIHGHIIGMGLSPDHRYLYVNSRSWPSGSVVSDPMQPPPIAEEIDLHVFDLKTMKE
          ..SDEF................MGLSPDHRYLYVNS.SWPSGSVV.DPMQPPPIAEEIDLHVFDLKTMKE
Retrocopy GHSDEFXXXXXXXXXXXXXXXXMGLSPDHRYLYVNSCSWPSGSVVLDPMQPPPIAEEIDLHVFDLKTMKE

Parental  VKRALRAHRAYT
          VKRALRAH...T
Retrocopy VKRALRAHCVVT

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	215.15 RPM
SRP007412_cerebellum	0.00 RPM	300.01 RPM
SRP007412_heart	0.00 RPM	504.36 RPM
SRP007412_kidney	0.00 RPM	280.49 RPM
SRP007412_liver	0.00 RPM	101.20 RPM
SRP007412_testis	0.00 RPM	1238.12 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1932 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1932 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	ENSMODG00000017319	1 retrocopy	retro_mdom_1932 ,