RetrogeneDB ID: retro_mdom_601

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:482587095..482588231(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RASSF8
• Ensembl ID: ENSMODG00000016548
• Aliases: None
• Description: Ras association (RalGDS/AF-6) domain family (N-terminal) member 8 [Source:HGNC Symbol;Acc:13232]

Sequence

>retro_mdom_601
TACACTAATAGAAAAAAATGGAGAGATACAGAGAGACACTTAGCACCTCATGAAAATCCAATCATTTCATTAAACAAATG
GGGACAATATGCCAGTGATTACAACTAATATTACATCGTACAGGGCCATCTCTTAGTGAGAGGCCAACTTCAGACAGTGT
TGCCCGAATACCTGAGAGAACTTTATATAGACAAAGCTTGCCCCCCTTGGATAAACTGAGGCCTCAAAATGACAAGTCAA
TAAAAAGGTGAGAGCCAAAAAGGAAGTCTTTGACATTTATAGGAGGTGTCAAAGGACTCATGGACATTTTTGCGAAAGGT
AAAGAAACCAAATTTAAACAAAAAGTTCTTAGTAACTGTAAGACAAAAGCATATAAATTAAAAAAGCTCACCCACTTCAG
GCAGAAAAGCTTCAATTCATTGAGAAGCAATTTGAATCCAATGACATGGAAATTAGGTACTGGGAACAAAAGAACAATTC
TAACCTGGAAGAAGAAATTGTTCATCTTGAGCAGAAGATCAAAAGAAATGATATAGAAATTAAAGAGGAAGAATTTTGGT
GAAATGAATTACAGATTGAACAAGAAAATGAAAAACAGCTGAAGGATAAGCTTCAAGAGATGAAGTAGAGTATCCTAGAA
TGTGAAGGCAAATTAAGGGACTTTTTGGCTCAAATCCACAGTATAGAAAGTGGTCTGGAAGCAGAAAAGTTACACGAGGA
AGTTCAAGAGTCACAGGTCAATGAAGTAGTGAAAAGAAAGATTGGTAAGGTCAAAGGAGAAATTGATATTCAGGGACAAC
AGAGTCTGGGGTTAGAAAATGGCATTAAAGCTGTAGAAAGACCTCTAGGGACAAGCCACCAAAAGGTTACAGGACAAAGA
ACAAGAGCTAGAACAATTGACTAAATAGGTTCAACAAGTCAATCTTCAACAGTTTATATAACAGACGGGAACAAAGGTTA
CAGTTCTTCCATCAGAGACCATCGAAGTGGAAGCCTCACATGCAGACATAGAAAGGGAGACATCATTCCAGTCTGGGTCC
TTGAAACATCCTGGTTCCTCTCTGCAGCTGCCCAGTAACCTTTGGATTCTACAGAATCCAATTTCATCTGGCTTTAATCC
TGAGGGCATATATGTA

Alignment

ORF - retro_mdom_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.47 %
• Parental protein coverage: 90.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTLIEKWRDTERHLAPHENPIISLNKWGQYASD-VQLILRRTGPSLSERPTSDSVARIPERTLYRQSLPP
          YT...KWRDTERHLAPHENPIISLNKWGQYASD..QLIL.RTGPSLSERPTSDSVARIPERTLYRQSLPP
Retrocopy YTNRKKWRDTERHLAPHENPIISLNKWGQYASD<LQLILHRTGPSLSERPTSDSVARIPERTLYRQSLPP

Parental  LAKLRPQNDKSIKRREPKRKSLTFTGGAKGLMDIFGKGKETEFKQKVLSNCKTTADELKKLIR-LQTEKL
          L.KLRPQNDKSIKR.EPKRKSLTF.GG.KGLMDIF.KGKET.FKQKVLSNCKT.A..LKKL...LQ.EKL
Retrocopy LDKLRPQNDKSIKR*EPKRKSLTFIGGVKGLMDIFAKGKETKFKQKVLSNCKTKAYKLKKLTH<LQAEKL

Parental  QSIEKQLESNDMEIRYWEQKYNSNLEEEIVRLEQKIKRNDVEIEEEEFWENELQIEQENEKQLKDQLQEM
          Q.IEKQ.ESNDMEIRYWEQK.NSNLEEEIV.LEQKIKRND.EI.EEEFW.NELQIEQENEKQLKD.LQEM
Retrocopy QFIEKQFESNDMEIRYWEQKNNSNLEEEIVHLEQKIKRNDIEIKEEEFW*NELQIEQENEKQLKDKLQEM

Parental  KQRILECEGKLKDYLAQIHSIESGLEAEKLHREVQESQVNEEEVKGKIGKVKGEIDIQGQQSLRLENGIK
          K..ILECEGKL.D.LAQIHSIESGLEAEKLH.EVQESQVN.E.VK.KIGKVKGEIDIQGQQSL.LENGIK
Retrocopy K*SILECEGKLRDFLAQIHSIESGLEAEKLHEEVQESQVN-EVVKRKIGKVKGEIDIQGQQSLGLENGIK

Parental  AVERSL-GQATKRLQDKEQELEQLTKELRQVNLQQFIQQTGTKVTVLPAEPIEVEASHADIEREASFQSG
          AVER.L.GQATKRLQDKEQELEQLTK...QVNLQQFI.QTGTKVTVLP.E.IEVEASHADIERE.SFQSG
Retrocopy AVERPL>GQATKRLQDKEQELEQLTK*VQQVNLQQFI*QTGTKVTVLPSETIEVEASHADIERETSFQSG

Parental  SLKRPGSSRQLPSNLRILQNPISSGFNPEGIYV
          SLK.PGSS.QLPSNL.ILQNPISSGFNPEGIYV
Retrocopy SLKHPGSSLQLPSNLWILQNPISSGFNPEGIYV

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	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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_601 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_601 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016548	1 retrocopy	retro_mdom_601 ,
Tarsius syrichta	ENSTSYG00000000655	1 retrocopy	retro_tsyr_1910,