RetrogeneDB ID: retro_mdom_1206

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:493251795..493252468(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012785
• Aliases: None
• Description: None

Sequence

>retro_mdom_1206
CCAGCAGAAAACCACTGTGTTGCCCCAAGGAAGACCCTACAAATAGTGACGAGCTCCCTGCTGACAGAAGCTGGGTTTGA
GAGTAGTGAGAAAGCAGAGTTGGAAACATCAATTGAGATATTACAAAGGTCCCTTTCAGACATTGGAATGAACGTTAAAT
CCTATTGGGAGCACATGGGCAGGACACAGGAAAAACTCTCAGATGCTGTAGTCACACTTGCTGAGATGTATTTTGATGTG
GAAACTCTCCCTGTATTTGCTAATAGATCCCAGAGGACAGTCGTCATATCAACTCCAGTCATCAAGAGACCCGAGGCTCC
CAATGTCCCAAGTGCTACACAGAACAGGGCTAACCCAGCTCATAACCCTAGCTATATCCCTACATTTCCAGATCCCCACA
CCTACATCAAAATACCTGCATGTTGCAAGTCTGTGCCAGATTACCAGGTCCTTCAGGAAAAGGCTGCATCAGAGAGGTGG
GATATGGAACAGGCACTTACTCGTTTTGTGTGCCAAGGCAGGCAAGACCCAGAGTCTTTTCAAAGATATCAATCCGTTCC
TACTGATCGCTGCCAAGCCACTTCCCATTGACTACCTGACAGCCCTTCTCCCATCTGAACTGGAGATGCAGCAGATGGAA
GAGACTGATTCTTCTGAACTAGGTGAACAGACA

Alignment

ORF - retro_mdom_1206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.72 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PADNYYLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSYLSEIGRSAKSYCEHTARTQPTLSDIV
          PA.N...A.R.TLQ.V.SSLLTEAGFES.EKA..ET..E.LQ..LS.IG...KSY.EH..RTQ..LSD.V
Retrocopy PAENHCVAPRKTLQIVTSSLLTEAGFESSEKAELETSIEILQRSLSDIGMNVKSYWEHMGRTQEKLSDAV

Parental  VTLVEMGFNVETLPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNKSHPPHIPSHFPEFPDPHTYIKTPT
          VTL.EM.F.VETLP..A.RSQR.V....PV...P..P....A.QN...P.H.PS..P.FPDPHTYIK.P.
Retrocopy VTLAEMYFDVETLPVFANRSQRTVVISTPVIKRPEAPNVPSATQNRANPAHNPSYIPTFPDPHTYIKIPA

Parental  YRELVSDYQVLREKAASQRRDVERALTRFM-AKTGETQSLFKDDVSTFPLIAARPFTIPYLTALLPSELE
          ....V.DYQVL.EKAAS.R.D.E.ALTRF..AK.G.TQSLFK.D...F.LIAA.P..I.YLTALLPSELE
Retrocopy CCKSVPDYQVLQEKAASERWDMEQALTRFV>AKAGKTQSLFK-DINPFLLIAAKPLPIDYLTALLPSELE

Parental  MQQMEETDSSEQDEQT
          MQQMEETDSSE..EQT
Retrocopy MQQMEETDSSELGEQT

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_1206 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1206 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206 , retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,