RetrogeneDB ID: retro_mdom_1222

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:15226366..15226969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000029355
• Aliases: None
• Description: None

Sequence

>retro_mdom_1222
ATGGTGGGGCTTTGTCGTCCCACAGAGGAGAGAACGGGCCGCCCTGCACTGGAGTCAGGAGGCTGTTGGGGGTGGCGCTG
GTCTGGGACCTTCTCCAAAGGGGACATTGAGGCGTACAAAGAAGCCTCTCCACCTTGGGGATCCCATCCCCTGAAGGACC
ACAGTTTGGCCCAAGCAGAGACCCCAGAGCCAGAGAGAATGGCCCCCAGGACCCAGAGGCCTCCTTCCCAGGGATCAATA
ACATTCAAGGATGTTGCTGTGAACTCAACCCAGGAAGAGTGGTGCCTGTTGGACCATTCTCAGAAAGAGCTGTAGCTGGA
GGTTGTGCTGGAGAATGTGCAGAATCTACTCTCTGTGGGGCTTCCAGTTCCTAAAGAAAATTTTATCTCCTCTTTTCAGC
AAGGAGAAGCACCATGGCTCCTAGAGCAAAAAGATCCAAGGAGTCCCTATCTAGAGCCAGAGACTAACTTTGAAGTGAAG
GAGATGTCTACAAAGCTGAGCCTTTTTGTGAGAGGATGTGGTCACCAAAGATGCATGAATGAGGGCCACTATGACTACAC
TTTGAGAGAAATCTATGGCAATAATATCAAAGTAAATAAAAAC

Alignment

ORF - retro_mdom_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.8 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLCLPPEETAGYLALEPEGYWGRGWFGPFSGGDVQAHREDVSPPWGC--LKDPRVTPAESPQPEGEAP
          M.GLC.P.EE..G..ALE..G.WG..W.G.FS.GD..A..E..SPPWG...LKD.....AE.P.PE..AP
Retrocopy MVGLCRPTEERTGRPALESGGCWGWRWSGTFSKGDIEAYKE-ASPPWGSHPLKDHSLAQAETPEPERMAP

Parental  GTPRPPSQGTITFKDVAVDFTQEEWDLLDQFQKELYLEVMLENVQNLLSVGLPVPRENFISCFQQGEAPW
          .T.RPPSQG.ITFKDVAV..TQEEW.LLD..QKEL.LEV.LENVQNLLSVGLPVP.ENFIS.FQQGEAPW
Retrocopy RTQRPPSQGSITFKDVAVNSTQEEWCLLDHSQKEL*LEVVLENVQNLLSVGLPVPKENFISSFQQGEAPW

Parental  LLEQKGPRSPYLEAETNFEVKEMSTELSLFVEGCGPQRYMDDGPCDFILRELYDSNINVNKN
          LLEQK.PRSPYLE.ETNFEVKEMST.LSLFV.GCG.QR.M..G..D..LRE.Y..NI.VNKN
Retrocopy LLEQKDPRSPYLEPETNFEVKEMSTKLSLFVRGCGHQRCMNEGHYDYTLREIYGNNIKVNKN

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_1222 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1222 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	ENSMODG00000029355	1 retrocopy	retro_mdom_1222 ,