RetrogeneDB ID: retro_mdom_1180

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:379167416..379168604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC7
• Ensembl ID: ENSMODG00000009718
• Aliases: None
• Description: DEP domain containing 7 [Source:HGNC Symbol;Acc:29899]

Sequence

>retro_mdom_1180
CCGGTGTTTGAGGACAGTAGCTGCAGCCTTTACCGCTTCATGGCCTTCCCTGGCCAGGAGGACAGGCAGGTGGGGAAGGA
GAACCAAGTGGGCCCAGCTGTCAAATATGAGAAGACACCATTATGTCATTCATCCGCTTTGAAGTCAACCAGCTTAGAGG
ATCTGTGGGAAAACCTGAGTTTGAAGCCAGCTAACTCCCCCCGTGTAAATATCTCCACAAATCTGTCTCCTCAAGTTATT
AATGAAGTATGGCAAGAAGAAACCATCGGGCGTCTGCTCCAGCTTATCAACCTCCTGCTCCTTGACTCCTTGCTTCAGCA
CCAGGACGCAGCCCCCAGAGCTCCGAAGCCCCGGCCTAGCCTGATCTGATAGCCACCAGCAACTACCTGGACCTAGGGGT
TCTCAAGGCCTACAGCGACACGCAGGATGAGGAATGTCTCTTGGCAGCAACGGACTGCTTAGAGTACCTTCTGGACCAGA
TGGTGGTGGAGCTGAGCAGAAATTTCCCTGAGCTTCCAGACAAAGGAGATGTGTGGAAGGTGCTCTTATTGGATGCCATT
AGTAAATACTACAACAATAGGGAACCTCTGTTAAACCACTTATTTGACGTCCACACGGGGATTGTAGAACTCCTAGTGAA
TGGGAAGATGGACAAAGTGCTACAAGCAACGGAGCTCTGCCTGAAGCTGTTAGATTCCCCCAGGTGAGAGGAGTTCCAAA
GAATTGCTGTACTTGATGGCCGGGGCAGCCCGTCCTTCAGAATTTAAGTTACAGAAAGAGAGTGATAATCGGATGGTGGT
GAAAAGGGCATTTTCCAAAGAGATTGTAAACAACAAAAATTTATCCAAAGGATAAACAGACCTTTTGATGCTATTTTTAG
TGGATCATCAAAAAGATGTTTTTAAGATCCCAGGAATGCTGCACAAAATCGTCAGTGATAAACTCATGGCCATACAAAGA
GGAAAAGAGCCAGAGAGAGACACAGGCTGCCACAGACATGACCAAAGTGAGTATCACAGCAATACCCAAAAAGCCACAAA
GGAAGAGCTTTTGTCTTTGCTAAAATCTATTGATGAGGATTCAAAAATATCTGCCAAAGAAAAGAAGAAATTGCTATGTC
AGTTTTATGAAAGCCACCAGAATATCTTTGTGGAATATTTTGGAGATAGAACTTCAAATATTTTTATA

Alignment

ORF - retro_mdom_1180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 76.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVFEDSSCSLYRFTAEPGREDGQAGKENRVRPAARYEKTPLCHSSALKSASLEDLWENLSLKPADSPRVN
          PVFEDSSCSLYRF.A.PG.ED.Q.GKEN.V.PA..YEKTPLCHSSALKS.SLEDLWENLSLKPA.SPRVN
Retrocopy PVFEDSSCSLYRFMAFPGQEDRQVGKENQVGPAVKYEKTPLCHSSALKSTSLEDLWENLSLKPANSPRVN

Parental  ISTHVSPQVINKVWREETIGRLLQLIDLPLLDSLLQQQDAAPRAPRP-PAQPDLIATSNYLDRGVLKAYS
          IST..SPQVIN.VW.EETIGRLLQLI.L.LLDSLLQ.QDAAPRAP.P.PA.PDLIATSNYLD.GVLKAYS
Retrocopy ISTNLSPQVINEVWQEETIGRLLQLINLLLLDSLLQHQDAAPRAPKP<PA*PDLIATSNYLDLGVLKAYS

Parental  DAQDDEWLSAATDCLEYLPDQMVVELSRNFPELPDKGDVWKALLFDAISKYYNNREPLLNHLFDVHTGIA
          D.QD.E.L.AATDCLEYL.DQMVVELSRNFPELPDKGDVWK.LL.DAISKYYNNREPLLNHLFDVHTGI.
Retrocopy DTQDEECLLAATDCLEYLLDQMVVELSRNFPELPDKGDVWKVLLLDAISKYYNNREPLLNHLFDVHTGIV

Parental  ELLVNGKMDKALEATQLCLKLLDSPRREEFRR-LLYLMAVAARPSEFKLQKESDNRMVVKRAFSKAIVNN
          ELLVNGKMDK.L.AT.LCLKLLDSPR.EEF.R.LLYLMA.AARPSEFKLQKESDNRMVVKRAFSK.IVNN
Retrocopy ELLVNGKMDKVLQATELCLKLLDSPR*EEFQR>LLYLMAGAARPSEFKLQKESDNRMVVKRAFSKEIVNN

Parental  KNLSKGKTDLLVLFLVDHQKDVFKIPGMLHKIVSDKLMAIQRGKEPERDTGYVFCQRHDQSEYHSNTQKA
          KNLSKG.TDLL.LFLVDHQKDVFKIPGMLHKIVSDKLMAIQRGKEPERDTG...C.RHDQSEYHSNTQKA
Retrocopy KNLSKG*TDLLMLFLVDHQKDVFKIPGMLHKIVSDKLMAIQRGKEPERDTG---CHRHDQSEYHSNTQKA

Parental  TKEELLSLLRTIDEDSKISAKEKKKLLRQFYESHQNIFVEYFGDRISNIFI
          TKEELLSLL..IDEDSKISAKEKKKLL.QFYESHQNIFVEYFGDR.SNIFI
Retrocopy TKEELLSLLKSIDEDSKISAKEKKKLLCQFYESHQNIFVEYFGDRTSNIFI

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_1180 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1180 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012405	1 retrocopy	retro_dnov_1210,
Echinops telfairi	ENSETEG00000017093	1 retrocopy	retro_etel_1447,
Loxodonta africana	ENSLAFG00000008704	1 retrocopy	retro_lafr_539,
Monodelphis domestica	ENSMODG00000009718	1 retrocopy	retro_mdom_1180 ,
Monodelphis domestica	ENSMODG00000019582	1 retrocopy	retro_mdom_149,