RetrogeneDB ID: retro_mdom_1250

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:102820245..102820658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001863
• Aliases: None
• Description: None

Sequence

>retro_mdom_1250
GTTATTGAATTGGTATCTTCTATGTCCCAATATTTCCATCCAGACTGTGAGTTTTCTACCAATAAGGTAATAAATTTGGA
GTTGTGTGCTAGCTATGTCTACTTCTCCATGGCTTATTATTTTAACTATCATGATATGGCCCTGAAACACTTCTCAAAGT
TCTTCTGAGAGCTGTCCAAAAAAGAAGCACATTCAGAAAAAAATTCTCTAGTACTTAATCAAAAGGGGAGGACATCCTAT
TCTGGAATATATCCTAAAGTCAGAGGTAAAAGATTGATTAGATGGCCTGAAGGCTCTTGTAGTTGAGAAGACTATTAAGG
AGGAATTGTTGGGTCTGTACAAATAAGGCAAAGGGGCATGAGGTTCCACCCTTTTGCCTTACTGTACAGAGCCAACAATT
GGAGTCTGAACTC

Alignment

ORF - retro_mdom_1250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 77.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIEMENSVFQHFHPECELSISKTINLELHAGYVYFSMTYYFGHHDVALKHFSMFFREQSKKKMKHAE-KI
          VIE...S..Q.FHP.CE.S..K.INLEL.A.YVYFSM.YYF..HD.ALKHFS.FF.E.SKK...H.E.KI
Retrocopy VIELVSSMSQYFHPDCEFSTNKVINLELCASYVYFSMAYYFNYHDMALKHFSKFF*ELSKKE-AHSE>KI

Parental  LQYLTKRGGHPVLENILKSEVQYWSDGLQALEEALVIEKAVNEELL-ILCNKAKEHEDPHLCGFLESELL
          L.YL.KRGGHP.LE.ILKSEV....DGL.AL....V.EK...EELL....NKAK.HE.P..C....S..L
Retrocopy L*YLIKRGGHPILEYILKSEVKD*LDGLKAL----VVEKTIKEELL>VCTNKAKGHEVPPFCLTVQSQQL

Parental  DEQV
          ....
Retrocopy ESEL

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_1250 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1250 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.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004685	1 retrocopy	retro_acar_188,
Monodelphis domestica	ENSMODG00000001863	5 retrocopies	retro_mdom_1250 , retro_mdom_302, retro_mdom_551, retro_mdom_789, retro_mdom_848,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Monodelphis domestica	ENSMODG00000013730	3 retrocopies	retro_mdom_1989, retro_mdom_6, retro_mdom_745,