RetrogeneDB ID: retro_mdom_369

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:298517235..298517836(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1B
• Ensembl ID: ENSMODG00000012099
• Aliases: None
• Description: anti-silencing function 1B histone chaperone [Source:HGNC Symbol;Acc:20996]

Sequence

>retro_mdom_369
ATGGCCAAAGTTTCTGTTCTGAAAGTATTGGTGCTAGAGAACTCTAGCCCTTTCCATAGCCCCTTCCAGTTCGAGATCAG
CTTCAAGTGCAGCGAGACCTTGGCCTATGACCTAAAATGGAAAATAATTTATGTGGGTTCAGCAGAGAGTGAGGAGTTTG
ACCCGATACTAGACTCAGTGCTAGTAGGACCAGTCCCAGCAGGGAGACAAATGTTTGCCTTTCCCTAATGCCTCCCTAAT
CCCAGAAACTTCATTGATTCAATGAGTGTAACTGTGGTCCTCATAACCTGCACCTAATATGGGTAGGAGTTCATCCGAGT
TGGCTAATATGTCAACAATGAATATACCAACCCTGAGCTTCAGGAGAACCCATTCCTGAAACCAGACTTCTCTCAGCTCC
AGCGAAACATCTTGGCTTCTAATCCTCAGGTGACTCAATTCCATATCAACTGGGACAGTACCACAGATAAATTAGAGGAC
ATTGAAAACCAAGATCCTGTCTTCAGCCTGGGACTCCCTTTGAGTTTTCCTCCAAACCAAAGGACTAGATCTTCCAGACT
GTGCCCCCAGCATCATTCCTGAAAATTCTATGAACTGCATC

Alignment

ORF - retro_mdom_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKVSVLNVSVLENPSPFHSPFQFEISFECSEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRH
          MAKVSVL.V.VLEN.SPFHSPFQFEISF.CSE.LA.DL.WKIIYVGSAESEEFD.ILDSVLVGPVPAGR.
Retrocopy MAKVSVLKVLVLENSSPFHSPFQFEISFKCSETLAYDLKWKIIYVGSAESEEFDPILDSVLVGPVPAGRQ

Parental  MFVFQADAPNASLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYTNPELRENPPLKPDFSQLQRNIL
          MF.F....PN...........VTVVLITCT..G.EFIRVG.YVNNEYTNPEL.ENP.LKPDFSQLQRNIL
Retrocopy MFAFP*CLPNPRNFIDS--MSVTVVLITCT*YG*EFIRVG*YVNNEYTNPELQENPFLKPDFSQLQRNIL

Parental  ASNPRVTRFHINWDSTTDKLEDIENQDPVLSLGLPLSCPP-TKGLDLPDCAPSIIPENSMDCI
          ASNP.VT.FHINWDSTTDKLEDIENQDPV.SLGLPLS.PP.TKGLDLPDCAPSIIPENSM.CI
Retrocopy ASNPQVTQFHINWDSTTDKLEDIENQDPVFSLGLPLSFPP>TKGLDLPDCAPSIIPENSMNCI

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_369 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_369 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004085	1 retrocopy	retro_btau_662,
Canis familiaris	ENSCAFG00000016482	1 retrocopy	retro_cfam_33,
Echinops telfairi	ENSETEG00000013713	1 retrocopy	retro_etel_379,
Myotis lucifugus	ENSMLUG00000000537	4 retrocopies	retro_mluc_1426, retro_mluc_2042, retro_mluc_2614, retro_mluc_775,
Monodelphis domestica	ENSMODG00000012099	4 retrocopies	retro_mdom_366, retro_mdom_367, retro_mdom_369 , retro_mdom_688,
Sorex araneus	ENSSARG00000000534	1 retrocopy	retro_sara_552,