RetrogeneDB ID: retro_mdom_1760

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:6884928..6885524(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE2
• Ensembl ID: ENSMODG00000010586
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 2 [Source:HGNC Symbol;Acc:6891]

Sequence

>retro_mdom_1760
AACAATTTTAAACTTCTACAAGCATCATTTAAAAGACTGAATGTTGATAAGGGTCATTTCAGTGGAGAAGCTAGTGAAAG
GGTGCTTTCAGGACAACTTGGATTCATCCAGTGGTTTAAGCAGTTCCATGATGCAAACTATGATGGGAAGGAGTATGACC
CTGTGGAGGCTCAGCAAGGTCAGAATGCAATTCCCCCAGCAGACTCCAGAGAATAGATCTTTAACTCACCCAAGAAATTG
TATCATGCAAACTCAGCAACAGCAGATACTTCAAAATATAGTCCAGCTTCTAAACCAGGATCTACTCCTCGTCCCTCATC
TGCAAGAAGGACCACATCTAGCCGGCGATCAGCCTCCAAATCCGAGAAAGAATTAGAAACCCAGGTCATACAGCTCAATG
AATGGGTACATTCATTAAAAGTTGCACTTGAAGGCATGGAGAAGGAAAGAGATTTCTACTTTGGGAAATTGAGAGAGATT
GAGCTAACCTGCCAAGAACATGTGCAGAGACTAATATATGCTTCAGACAAATAGGAAAGCCACACGAGGAGCCAGAAGCA
GAGGAACAAGTCCATGAGCAGCCTCAGCAAAAGGAA

Alignment

ORF - retro_mdom_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.95 %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HNFKLLQASFKRMNVDK-VIPVEKLVKGRFQDNLD-FIQWFKKFYDANYDGKEYDPVEARQGQDAIPPPD
          .NFKLLQASFKR.NVDK.VI.VEKLVKG.FQDNLD.FIQWFK.F.DANYDGKEYDPVEA.QGQ.AIPP.D
Retrocopy NNFKLLQASFKRLNVDK>VISVEKLVKGCFQDNLD<FIQWFKQFHDANYDGKEYDPVEAQQGQNAIPPAD

Parental  PGEQIFNLPKKSHHANSPTAGAAKSSLASKPGSTSSRPSSAKRTPSSSGSASKSEKDLETQVIQLNEQVH
          ..E.IFN.PKK..HANS.TA...K.S.ASKPGST..RPSSA.RT.SS..SASKSEK.LETQVIQLNE.VH
Retrocopy SRE*IFNSPKKLYHANSATADTSKYSPASKPGSTP-RPSSARRTTSSRRSASKSEKELETQVIQLNEWVH

Parental  SLKLALEGMEKERDFYFGKLRDIELICQEHGQ-ENDDLMQRLMEVLYASDEQESHTEEPEAEE
          SLK.ALEGMEKERDFYFGKLR.IEL.CQEH.Q.E..................E...E.P...E
Retrocopy SLKVALEGMEKERDFYFGKLREIELTCQEHVQ<ETNICFRQIGKPHEEPEAEEQVHEQPQQKE

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_1760 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1760 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010586	1 retrocopy	retro_mdom_1760 ,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Pteropus vampyrus	ENSPVAG00000012260	1 retrocopy	retro_pvam_1236,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,