RetrogeneDB ID: retro_mdom_1647

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:40666982..40667553(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG4
• Ensembl ID: ENSMODG00000014496
• Aliases: None
• Description: B-cell translocation gene 4 [Source:HGNC Symbol;Acc:13862]

Sequence

>retro_mdom_1647
TGGTATCCAGATATTCCTTCTAAAGGGCAAGCTTTCAGGTATATCAGGATAAATAAAAACAGAAAAAAGATCCCCTTCTG
GAGAGGGCATGTGCTGAAAGTAATGTGAATTTTTTTCACCTGGGACTTCCAAAGGGAATGACCATATGGGTAGATCCCTT
TGAAGTGTGCTGCAGGTATGGCAAGAAAAATCATCCCTTTATAGTTTCTTGTTTTAATGGCAGGCAGAAAGAATGGGAAA
TGTCTCAACAGATCAGTCATGATATTAATAATGTCACATCTGACTATTATTCTGGCACTTCCTCTGATGAAGATACATGT
GGCAGAGAGCCTCAAGTAATTCCTAAATCAGAAATTCAAAAAGCATTTATCAGGTTGAGAATTTCAAGCAGCTCCTCCAA
ATTTGGTTCCAATATTCCCATAAAAATAATATAACTGATGGGCACCCCAATCTCCCAGGAAATACATTATATGTCCCATA
CAAGATCCACAAATGCTACAGGTCTGCTCCTGTGTTTCCAGGACCCTGAGTGGATAAGTACCACTGGGTCAACACAAATC
AGCAAAGTACC

Alignment

ORF - retro_mdom_1647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.49 %
• Parental protein coverage: 74.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WYPDIPSKGQAFRCIRINK-QQKKDPLLERACAESNVNFFHLGLPKEMTIWVDPFEVCCRYGEKNRPFIV
          WYPDIPSKGQAFR.IRINK..QKKDPLLERACAESNVNFFHLGLPK.MTIWVDPFEVCCRYG.KN.PFIV
Retrocopy WYPDIPSKGQAFRYIRINK<KQKKDPLLERACAESNVNFFHLGLPKGMTIWVDPFEVCCRYGKKNHPFIV

Parental  ACFNGRQEEWEISQQITHAINKVTSDYYSGTSSDEDTCGREPQVIPK-VRNPKSIYQVEYFKQPLQTWFQ
          .CFNGRQ.EWE.SQQI.H.IN.VTSDYYSGTSSDEDTCGREPQVIPK..RN.KSIYQVE.FKQ.LQ.WFQ
Retrocopy SCFNGRQKEWEMSQQISHDINNVTSDYYSGTSSDEDTCGREPQVIPK<IRNSKSIYQVENFKQLLQIWFQ

Parental  YSRKKNMTDGRPNLPGSTLYVPYKIHKCYRPAAVFPGPRVDKYHWVNTNRQSS
          YS.K.N.TDG.PNLPG.TLYVPYKIHKCYR.A.VFPGP.VDKYHWVNTN.QS.
Retrocopy YSHKNNITDGHPNLPGNTLYVPYKIHKCYRSAPVFPGP*VDKYHWVNTNQQST

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_1647 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1647 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014210	2 retrocopies	retro_cfam_1324, retro_cfam_471,
Choloepus hoffmanni	ENSCHOG00000000032	1 retrocopy	retro_chof_2674,
Equus caballus	ENSECAG00000012564	1 retrocopy	retro_ecab_299,
Monodelphis domestica	ENSMODG00000014496	1 retrocopy	retro_mdom_1647 ,
Sus scrofa	ENSSSCG00000015020	1 retrocopy	retro_sscr_680,
Tursiops truncatus	ENSTTRG00000010435	1 retrocopy	retro_ttru_1303,