RetrogeneDB ID: retro_mdom_607

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:506745949..506746364(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D2
• Ensembl ID: ENSMODG00000002896
• Aliases: None
• Description: SFT2 domain containing 2 [Source:HGNC Symbol;Acc:25140]

Sequence

>retro_mdom_607
TTGACTAAAGTAACTAAAACAGCATAATTAAGTTAGGGCACAAGAATAAGAGACTTTGCTGCTTATTTTACTTTAGGGAT
TCTTTTCTTGTCCCTGGTACTTTTCTGCTACAGATGCCTTGGAAAGGCTTTATCTTTTTTTGCAGTATTTTATGCCTTGG
GGAACACTGCATCACCTGAGAGTATTCTTTCTTATGGGACCAATGAAGCAGCTGAAATGTATGTTTAAGTCTACTTGACA
GATATGCACCAATGTGATGCTGTTGCATCTTGTATTCACCCTATGTTATGCCTTCTGGTGGCACAACAAAGAACTTGTTC
TCATTTTCTGCATTTCAGGGTCTTTGGCCTTGAAGTGGTACATATAGCCTTTCTTTTATATCACTTGGAAGGGATGCTGT
GAAAAGAAATGTTTT

Alignment

ORF - retro_mdom_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.23 %
• Parental protein coverage: 84.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAEVIETPSLSWGTRIKGFAACFAIGIIFSLM-GTFFLWVPKKGLVLF-AAFYTL-GNIASLGSTIFLMG
          L..V..T..LS.GTRI..FAA.F..GI.F....GTF.L..P.KG...F.A.FY.L.G....L....FLMG
Retrocopy LTKVTKTA*LS*GTRIRDFAAYFTLGILFLSL<GTFLLQMPWKGFIFF>AVFYAL>GTLHHL-RVFFLMG

Parental  PVKQLKRMFETTRLIATIVMLLCLILTLCSAFWWHNKGLALIFCILQSLALTWY--SISYIPFARDAVKK
          P.KQLK.MF..T..I.T.VMLL.L..TLC.AFWWHNK.L.LIFCI..SLAL.WY.....YI.......KK
Retrocopy PMKQLKCMFKST*QICTNVMLLHLVFTLCYAFWWHNKELVLIFCISGSLALKWYI*PFFYITWKGCCEKK

Parental  CF
          CF
Retrocopy CF

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_607 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_607 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607 ,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133,