RetrogeneDB ID: retro_mdom_356

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:273801285..273802142(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010142
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD4
• Ensembl ID: ENSMODG00000010390
• Aliases: None
• Description: programmed cell death 4 (neoplastic transformation inhibitor) [Source:HGNC Symbol;Acc:8763]

Sequence

>retro_mdom_356
GTCCAAAGGGGAAGTCACTGGACAGGCGGTCCCGGTCTGGGAAAGGAAGGTGGTGCAGGAGGCAAAGATGTATGGGGTAC
CCTGGTCAGGTGTATGATGTGAAAGAAGTAGATGTTAAAGATCCCAATTATGATGATGACCAGGAGAACTGTGTGTCTGA
AACAGTAGTTCTACCTTTGGATGAAAGGGCATGTGAGAAGACTTTAACAGCAATCATACAAGAATATTTTGAACGTGGAG
ATACTAATGAAGTTGCAGAAATGCTAAGGGATGAAATCTTGGTGAGATGAAAAGTGGAGTACCAGTGTTGGCAGTGTCCT
TGGCCTTGGAGGGAAAAGCCAATCATAGAGAAATGACATCTAAGCTCCTTTCTGACCTTTGTGGGACAGTAGTCAGCACA
AATGATGGAGAAAAATCATTTGATAAATTGCTTAGAGAACTACCAGAATTAGCATTACATACTCCTAGAGCACCACAGTT
GGTGGGACAATTGATTGCTAGAGCTGTTGGAGATGGAATTTTATTGCAATACTTACATTGATAGCTACAAAGGAACTGTA
GATTGGGTTCAAGCTCAAGCCACCCTGGACAGAGCTACAGTGCTTCTGAGCATAACAAAAGGTGAAAAGTGTAAAGCTAG
TGTGTGGGGTTCTGGAGGTGGGCAGCAATCAGTCAATCGTCTTGTTAAAGAGATTGGCATGCTGCTGAAAGAATACTTAG
TTTCTGGAGATTTATGTGAAGTTGAACATTGCCTTAAAGAACTAGAAATACCTCATTTTCACCATGAACTTGTGTATGAA
GCGGTTGTGATGGTTCTGGAGTCAACTGGAGAAAGCACATTTGAGATGGTACTGGAT

Alignment

ORF - retro_mdom_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 60.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDRRSRSGKGRGLPKKGGAGGKGVWGT-PGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDERAFEKTL
          ..R.S....G.GL.K.GGAGGK.VWGT.PGQVYDV.EVDVKDPNYDDDQENCV.ETVVLPLDERA.EKTL
Retrocopy VQRGSHWTGGPGLGKEGGAGGKDVWGT<PGQVYDVKEVDVKDPNYDDDQENCVSETVVLPLDERACEKTL

Parental  TPIIQEYFEHGDTNEVAEMLRDL-NLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVVSTNDVE
          T.IIQEYFE.GDTNEVAEMLRD..NLGEMKSGVPVLAVSLALEGKA.HREMTSKLLSDLCGTVVSTND.E
Retrocopy TAIIQEYFERGDTNEVAEMLRDE<NLGEMKSGVPVLAVSLALEGKANHREMTSKLLSDLCGTVVSTNDGE

Parental  KSFDKLLKELPELALDTPRAPQLVGQFIARAVGDGIL-CNTYIDSYKGTVDCVQARAALDRATVLLSMTK
          KSFDKLL.ELPELAL.TPRAPQLVGQ.IARAVGDGIL.CNTYIDSYKGTVD.VQA.A.LDRATVLLS.TK
Retrocopy KSFDKLLRELPELALHTPRAPQLVGQLIARAVGDGIL>CNTYIDSYKGTVDWVQAQATLDRATVLLSITK

Parental  GGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAVVMVLESTG
          G.K.K.SVWGSGGGQQSVN.LVKEI.MLLKEYL.SGD..E.EHCLKELE.PHFHHELVYEAVVMVLESTG
Retrocopy GEKCKASVWGSGGGQQSVNRLVKEIGMLLKEYLVSGDLCEVEHCLKELEIPHFHHELVYEAVVMVLESTG

Parental  ESTFKMVLD
          ESTF.MVLD
Retrocopy ESTFEMVLD

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	150.66 RPM
SRP007412_cerebellum	0.00 RPM	98.26 RPM
SRP007412_heart	0.00 RPM	317.77 RPM
SRP007412_kidney	0.00 RPM	292.34 RPM
SRP007412_liver	0.50 RPM	819.68 RPM
SRP007412_testis	1.38 RPM	738.59 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_356 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_356 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010390	1 retrocopy	retro_mdom_356 ,
Otolemur garnettii	ENSOGAG00000012583	1 retrocopy	retro_ogar_2211,