RetrogeneDB ID: retro_mdom_1443

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:77112159..77112831(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021248
• Aliases: None
• Description: None

Sequence

>retro_mdom_1443
CCAATAAATTGTCCACCTGGACTTGAATACTTAAGTGTGTTAGACAACTTACTGATCTTTCAGCAAATTGAATTTCTGGA
AGCACTCACAGGTTTTGAAACCAACAACAGATATGAAATTAAGAACCTCTTTGGGCAGAGAATTTACTATGCAGTGGAGG
AAAATGATTTCTGTACTCGAAACTGCTGTGGATCCTTAAGACCTTTTGTTATAAAGATTCTGGACTATTCATCCCATGAA
GTGATACATATTGAGAGGCCTTTAAAATGTGCTTCCTGTTATTTCCCCTGCTGCCTGCAAAAGTTGGAAATACAGTCTCC
TCCTGGTTCACCAATAGGTTATATTGTCCAAAAATGGCACCCATTTCTGCCAAAGTTTACAGTTCTAAATGAGCGCCATG
AGAAGGTGTTGACAATAGTTGGCCCATATATTGTTAGCAGTTGTTTCTCAAACATTGACTTTAATATAAAATCTCTTAAT
GAAAAGGTTATAGTTGGGAAAATTACAAAACAATGGTCAGGATTTTTTAAAGAAACATTTACCGATGCTGATAACTTTTC
AATTCAATTCCCACTAGACCTTGATGTGAAAATGAAGGCTGTCATGCTGGGTGCTTGCTTCCTTATTGACCTGCTGTTTT
TTGAAGTTGGTGGCACAAAGGCAGGAGTATGG

Alignment

ORF - retro_mdom_1443 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.09 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMNCPPGLEYLTQIDQLLIHQQIELLEVLTGFETNNKYEIKNSLGQRVYFAAEENDFCTLNCCGSLRPFV
          P.NCPPGLEYL...D.LLI.QQIE.LE.LTGFETNN.YEIKN..GQR.Y.A.EENDFCT.NCCGSLRPFV
Retrocopy PINCPPGLEYLSVLDNLLIFQQIEFLEALTGFETNNRYEIKNLFGQRIYYAVEENDFCTRNCCGSLRPFV

Parental  IKILDYSNREVIQIERPLRCSSCYYPCCLQKMEIQSPPGVPIGYVVQKWHPFLPKFAVLNEHQEEVLKIV
          IKILDYS..EVI.IERPL.C.SCY.PCCLQK.EIQSPPG.PIGY.VQKWHPFLPKF.VLNE..E.VL.IV
Retrocopy IKILDYSSHEVIHIERPLKCASCYFPCCLQKLEIQSPPGSPIGYIVQKWHPFLPKFTVLNERHEKVLTIV

Parental  GPCVACSCCSNIDFDVKSLNEDAIVGKITKQWTGFVKEAFTDADNFSIQFPIDLDVKMKAVMLGACFLID
          GP....SC.SNIDF..KSLNE..IVGKITKQW.GF.KE.FTDADNFSIQFP.DLDVKMKAVMLGACFLID
Retrocopy GPYIVSSCFSNIDFNIKSLNEKVIVGKITKQWSGFFKETFTDADNFSIQFPLDLDVKMKAVMLGACFLID

Parental  FMFFEKSGGNHSRASVW
          ..FFE..G.....A.VW
Retrocopy LLFFEVGG---TKAGVW

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_1443 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1443 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000027005	1 retrocopy	retro_fcat_797,
Myotis lucifugus	ENSMLUG00000008749	1 retrocopy	retro_mluc_1779,
Monodelphis domestica	ENSMODG00000021248	2 retrocopies	retro_mdom_1443 , retro_mdom_1597,
Mus musculus	ENSMUSG00000032369	1 retrocopy	retro_mmus_462,
Rattus norvegicus	ENSRNOG00000033412	1 retrocopy	retro_rnor_1962,