RetrogeneDB ID: retro_mdom_688

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:102482179..102482692(+)
• Located in intron of: ENSMODG00000009507

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_688
AGCGAGGCCTTGGTCGACGCCCTAGAATGGAAAATAATTTATGTGGGTTCAGCAGAGAATGAGGAGTTTGACCAGATACT
AGACTCAGTGCTAGTAGGGCTAGTCCCAGCAGGGAGACACATGTTTGTCTTTCAGGCAGATGTCCCTAACACTTCCCTAA
ACCCAGAAACTGATTCAGTGGGTGTAACTGTGGTCCTCATAACTGGTACCTACCATGGGCAGGAGTTCATCCCAGTTGGG
TACTATGTCAACAATGAATATACCAACCCTGACTTCAGGAGAACCCAACCCTGAAACCAGATTTCTCTGAGCCCCATTGA
AACATGACTTCTAATCCCTGGGTGACTCGATTCCATATCAACTGGGACAGTACCACAGATAAATTGGAGGACATTGAAAA
CCAAGATCCTGTCTTAAGCCTGGGGCTCCCTTTGAATTGTCCCCCAACAATAAGGGCTAGATTTTCCAGACTGTGCCCCC
AGCATCATTCCTGAAAATTCCATGGGCTGCATC

Alignment

ORF - retro_mdom_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 85.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRHMFVFQADAPNASLIPETDAVGVTVVLITCT
          SEAL.D.LEWKIIYVGSAE.EEFDQILDSVLVG.VPAGRHMFVFQAD.PN.SL.PETD.VGVTVVLIT.T
Retrocopy SEALVDALEWKIIYVGSAENEEFDQILDSVLVGLVPAGRHMFVFQADVPNTSLNPETDSVGVTVVLITGT

Parental  YHGQEFIRVGYYVNNEYTNPE-LRENPPLKPDFSQLQRNILASNPRVTRFHINWDSTTDKLEDIENQDPV
          YHGQEFI.VGYYVNNEYTNP..L.ENP.LKPDFS....N...SNP.VTRFHINWDSTTDKLEDIENQDPV
Retrocopy YHGQEFIPVGYYVNNEYTNPD<LQENPTLKPDFSEPH*N-MTSNPWVTRFHINWDSTTDKLEDIENQDPV

Parental  LSLGLPLSCPPTK-GLDLPDCAPSIIPENSMDCI
          LSLGLPL.CPPT..GLD.PDCAPSIIPENSM.CI
Retrocopy LSLGLPLNCPPTI>GLDFPDCAPSIIPENSMGCI

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_688 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_688 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,