RetrogeneDB ID: retro_mdom_324

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:135640335..135640787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF2
• Ensembl ID: ENSMODG00000018113
• Aliases: None
• Description: myeloid leukemia factor 2 [Source:HGNC Symbol;Acc:7126]

Sequence

>retro_mdom_324
TGCCAGACTTTTTCATCCTCCACTGTCATTTCCTATTCAAACCTGGATGATGATGTTCCCAAAGTCTACCAAGAAACATC
TGAGATGTGCTCAGCACGAGATGGGATCCAGGAGACAAGGAGCACCATGAGGGACTGTGATAGCAGACTAGAAAAGATGT
CCATTGGGTATCACATCTGAGACAGGGCAAACGTCCCTCAGTGTTCCTGAAATCACCTAACTGGGGACCAGGAAGAACAG
CAGGGTTACATCAATTTGGATGAGAGTGATGCTGAAGCATTTGACAAAGAGTGGACACAAGAGACATTCCAATACCAGCC
ACAACATCTCCTGGAATTTCATCCGCATGAGGCTACTGGAACGGGCCAGGGTAGAAGGACTGAGGGATGCTCTTGGCTAA
CTATACAGGGCCCTGAGGACTCCCCTTCCCAATAGTCAGATTCTATGACTGG

Alignment

ORF - retro_mdom_324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.71 %
• Parental protein coverage: 60.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CQTFSSSTVISYSNLGDGAPKVYQETSEMRSAPGGIRETRRTVRDSDSGLEQMSIGHHIRDRAHILQRSR
          CQTFSSSTVISYSNL.D..PKVYQETSEM.SA..GI.ETR.T.RD.DS.LE.MSIG.HI.DRA...Q.S.
Retrocopy CQTFSSSTVISYSNLDDDVPKVYQETSEMCSARDGIQETRSTMRDCDSRLEKMSIGYHI*DRANVPQCS*

Parental  NHRTGDQEERQDYINLDESDAEAFDNEWRRETSRYRPQRPLEFRRHEATGAGGGRRAEGPPRLAIQGPED
          NH.TGDQEE.Q.YINLDESDAEAFD.EW..ET..Y.PQ..LEF..HEATG.G.GRR.EG...L.IQGPED
Retrocopy NHLTGDQEEQQGYINLDESDAEAFDKEWTQETFQYQPQHLLEFHPHEATGTGQGRRTEGCSWLTIQGPED

Parental  SPSRQS-RRYDW
          SPS..S.R.YDW
Retrocopy SPSQ*S<RFYDW

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	0.24 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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_324 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_324 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000758	2 retrocopies	retro_dnov_1602, retro_dnov_649,
Echinops telfairi	ENSETEG00000014471	2 retrocopies	retro_etel_1236, retro_etel_233,
Microcebus murinus	ENSMICG00000010652	1 retrocopy	retro_mmur_449,
Monodelphis domestica	ENSMODG00000018113	1 retrocopy	retro_mdom_324 ,
Mus musculus	ENSMUSG00000030120	1 retrocopy	retro_mmus_1090,
Otolemur garnettii	ENSOGAG00000005976	1 retrocopy	retro_ogar_232,
Procavia capensis	ENSPCAG00000001026	1 retrocopy	retro_pcap_326,
Ictidomys tridecemlineatus	ENSSTOG00000009908	1 retrocopy	retro_itri_1707,