RetrogeneDB ID: retro_mdom_403

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:409824990..409825868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL45
• Ensembl ID: ENSMODG00000012560
• Aliases: None
• Description: mitochondrial ribosomal protein L45 [Source:HGNC Symbol;Acc:16651]

Sequence

>retro_mdom_403
CACCAGAGTTTAGAAGCCTTGTTCAGCCCAGTCTGTGTCACCCAGCCCATCACTTTGATCCCAATGAGAACCAAGAAGCT
CTTTATACCTCCTATTTATGAGCCTAAATACAAAACTGAGAAGGAGTTTCAGGACTGAGCCTGTGCTGCAGGGATTGTCA
TTCCCAAATAACGTCTTGAGTGTCCCATTCATTTGGCCTGCACAGCTGGGATTTTTGATGCCTATGTTCCTCCTGAGGTG
GATGTCCTACTAACATCCCTCTCCAAGTCTGGCTTGCAGCAAAAAACCGAGAAGCTAAAGCAAGGCAAGGCCTCACAGTT
GGCAATTCGGAAAGTTAGAGAATATGATGCTAATTTCCGTACCAATACCTTCCCAGAATAAGATTAGCAGATCTTTATTG
AAGCTCATCAATGCCTTAATACTTCAGATCATGACCGACTTCATGCCCTGGTAACTGAGTGCTGTTTCCCAGAGATGGTG
TGGGATGTCCAACTTAAGACAGTACATTGGAGCTTTATGGAATCTATGGAACCACCAAGAGTAGTTCATGTTTGTTGTCC
AAATATGGTGAGCAAGGGCAACATATATGGCCAGGTCACCGTCTACATGCACACTCTCCAGACCCTGGCTATCTATGAAC
GGTTTGGGTGGTTGATGTATGGACAAGAAGATGTGCCCAAGGATGTGTTGGAGTATGTGGTATTTGAGAGACACTTAACA
AACCCATAGGGGGCCTGGAGAATGCATGGAAAATTGTCCCTGCTTGGGCCCCTGCTAAGGATCCCATCCCCAAGACGGTG
ATGATTCCTGGTCCCAAGCTCCAACCATGGGAAGTGAATGTGGAAATTCAAAAGTCTCAGCCTGTTCAATGGCACAAG

Alignment

ORF - retro_mdom_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.58 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YPSLEAFFCPVRVTQHITLIPMRTKKRFIPPIYEPKYKTEKEFQDRARAAGIVIPKERLERPIHLACTAG
          ..SLEA.F.PV.VTQ.ITLIPMRTKK.FIPPIYEPKYKTEKEFQD.A.AAGIVIPK.RLE.PIHLACTAG
Retrocopy HQSLEALFSPVCVTQPITLIPMRTKKLFIPPIYEPKYKTEKEFQD*ACAAGIVIPK*RLECPIHLACTAG

Parental  IFDAYVPPEGDARLTSLSKAGLQQKTEKLKQGVASQLAIRKVREYDADFRTKTFPEKAQQIFVEAHQCLN
          IFDAYVPPE.D..LTSLSK.GLQQKTEKLKQG.ASQLAIRKVREYDA.FRT.TFPE...QIF.EAHQCLN
Retrocopy IFDAYVPPEVDVLLTSLSKSGLQQKTEKLKQGKASQLAIRKVREYDANFRTNTFPE*D*QIFIEAHQCLN

Parental  TSDHDRLHALVTERCFPEMVWDIQLKTVHWNFVESLEPPRVVHVRCPNMVSEGNIYGQVTVRMHTRQTLA
          TSDHDRLHALVTE.CFPEMVWD.QLKTVHW.F.ES.EPPRVVHV.CPNMVS.GNIYGQVTV.MHT.QTLA
Retrocopy TSDHDRLHALVTECCFPEMVWDVQLKTVHWSFMESMEPPRVVHVCCPNMVSKGNIYGQVTVYMHTLQTLA

Parental  IYDRFGRLMYGQEDVPKDVLEYVVFERHLTNPYGAWRMHG-KIVPAWAPAKDPIPKTVMIPGPKLQPWEE
          IY.RFG.LMYGQEDVPKDVLEYVVFERHLTNP.GAWRMHG.KIVPAWAPAKDPIPKTVMIPGPKLQPWE.
Retrocopy IYERFGWLMYGQEDVPKDVLEYVVFERHLTNP*GAWRMHG<KIVPAWAPAKDPIPKTVMIPGPKLQPWE-

Parental  YEEVNVEVQKSQPVQWHK
          ...VNVE.QKSQPVQWHK
Retrocopy ---VNVEIQKSQPVQWHK

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.50 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_403 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_403 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
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403 ,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,