RetrogeneDB ID: retro_mdom_1462

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:177047294..177047755(+)
• Located in intron of: ENSMODG00000020598

Retrocopy information

• Ensembl ID: ENSMODG00000020600
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM18
• Ensembl ID: ENSMODG00000019688
• Aliases: None
• Description: RNA binding motif protein 18 [Source:HGNC Symbol;Acc:28413]

Sequence

>retro_mdom_1462
TACCACTTCCTCAAACTCCTTCAGAAATTTGGCAAAGTAAAGCAATTTGACTTTCATTTCCACAAATCTGGTGCCTTGGA
AGGACAGCCCCGAGGGGAGGTATTGTTTTGTCAACTTTGAAAACAAACAGGAAGCAGAGCAAGTCATCTGGTGTCTTAAT
GGCAAGCTGGCCCTTTCTAAGAAGCTGGTGGTACCGCGGGCACATGCTCAAGTCAAGAGATATGATCATAACAAGAATGA
CAAAATCCTTCCAATCAGTCTTGAGCCATCATCAAACACTGAACCCAGTCAGTCCAACTTAAGCGTCAGTTCAAAGATAA
AAGCAATTGAAGCCAAGCTGAAAATGATGGTCGAAAAACCTGATGCTGAGTACTCAGCAGCCCCTGTCTATTCCTACTTC
AAACCACCAGATAAAAAAAAGGACTAGTCCTTAGTCCCGAACTGCTTGGAAGTCTCGAAGA

Alignment

ORF - retro_mdom_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YHLLKLLQKFGKVKQFDFLFHKSGALEGQ-PRG-YCFVNFETKQEAEQAIQCLNGKLALSKKLVVRWAHA
          YH.LKLLQKFGKVKQFDF.FHKSGALEGQ.P.G.YCFVNFE.KQEAEQ.I.CLNGKLALSKKLVV..AHA
Retrocopy YHFLKLLQKFGKVKQFDFHFHKSGALEGQ>PEGRYCFVNFENKQEAEQVIWCLNGKLALSKKLVVPRAHA

Parental  QVKRYDHNKNDKILPISLEPSSSTEPSQSNLSVSAKIKAIEAKLKMMAENPDAEYSAAPVYSYFKPPD-K
          QVKRYDHNKNDKILPISLEPSS.TEPSQSNLSVS.KIKAIEAKLKMM.E.PDAEYSAAPVYSYFKPPD..
Retrocopy QVKRYDHNKNDKILPISLEPSSNTEPSQSNLSVSSKIKAIEAKLKMMVEKPDAEYSAAPVYSYFKPPD>X

Parental  KRTSPYSRTAWKSRR
          ..TSP.SRTAWKSRR
Retrocopy XXTSP*SRTAWKSRR

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	103.94 RPM
SRP007412_cerebellum	0.00 RPM	104.14 RPM
SRP007412_heart	0.00 RPM	168.65 RPM
SRP007412_kidney	0.00 RPM	104.03 RPM
SRP007412_liver	0.00 RPM	75.02 RPM
SRP007412_testis	0.00 RPM	385.01 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1462 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1462 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013811	1 retrocopy	retro_cpor_237,
Myotis lucifugus	ENSMLUG00000004794	1 retrocopy	retro_mluc_298,
Monodelphis domestica	ENSMODG00000019688	1 retrocopy	retro_mdom_1462 ,
Oryctolagus cuniculus	ENSOCUG00000008527	1 retrocopy	retro_ocun_290,
Otolemur garnettii	ENSOGAG00000015104	1 retrocopy	retro_ogar_846,
Ochotona princeps	ENSOPRG00000010381	2 retrocopies	retro_opri_1123, retro_opri_360,
Ictidomys tridecemlineatus	ENSSTOG00000022388	1 retrocopy	retro_itri_1882,
Tupaia belangeri	ENSTBEG00000016520	1 retrocopy	retro_tbel_2898,