RetrogeneDB ID: retro_mdom_624

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:566145640..566146557(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD4
• Ensembl ID: ENSMODG00000001804
• Aliases: None
• Description: major facilitator superfamily domain containing 4 [Source:HGNC Symbol;Acc:25433]

Sequence

>retro_mdom_624
AACCTGCAGCCCGCGCTCACCTACTGGAGCGTCTTCTTCAGATTCGGCCTCTGCATGGGCTTCCTGGGGCCCGCGGTGTC
TGACCTGTGCTGCCAGACCCACGGCTCGCTGCCCCAGATCTCCTGGGTTTTCTTCTCGAAGCTGTTCTGTCTTTTGCTGG
GCAGCGCTCTGGGGGGCATCTTCAAGAGGATGCTGGCCAAGTCACTGTGGATCCTCTTTGCCTCATCTCTGACCATCTCA
CTAGTGTCTGCTGTCATCCCCTTCTGCCAAGATGTGGTGGTGTTGGCTACATCACAGCCAGAGCTGGTCTGGCCATGGGA
TTCATAGGCACAGTGGCCAACATGCAGTTGGTGAAGATCTACCAAAAGGATTCTGCTGTCTTCCTCCAGGTTCTACATTT
TTTTGGTGGGCTTTGGTGCCTTTCTGAGCCCCCTCATCGCTGACCCCTTCCTTTCTGAGAATGATTGTCTGCCAACCAAT
GCCACGAGCCATGACAGAGACGGCAGCTCCCATTTCCAAAAAATCTTGACACTCCACCATGCTCAGCCCAACCTGAGCCA
CCATGAGCTGCCTGCCATGCCTGGGTAGGGAATCCGATGTCGTCTTATGCCTTCTGGATCATGGCCTTGATCAATCTGCC
AGTGCCCATTTCTGTTCTGTTCCTGCTATGCAAGAGAAGGCTGGTGTCCTGTTGTCCAAGGAAAAAACCTCTGCTAGTGA
AGACTGATGAGCTTGCCCTTCAAATGGAGCTGCCTGAGAAGGAAGATTCCCCTCCTCTGCCAACCAAAGCACTGCCAGAG
ACAGGGCATGGAGACCTTTTCAGCCATTGTCAGAAGAAGGATTTTCAAGGAGTCTCTTGTTCCTTCTTTGCCATTCACAT
CACTGCAGCCCTGGTGCTATTCATGACTGATGGAATT

Alignment

ORF - retro_mdom_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.41 %
• Parental protein coverage: 59.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NLQPTLTYWSVFFSFGLCMGFLGPTVSDLRCQTHSSLPQISWVFFSQQFCLLLGSALGGFFKKTLAKSLW
          NLQP.LTYWSVFF.FGLCMGFLGP.VSDL.CQTH.SLPQISWVFFS..FCLLLGSALGG.FK..LAKSLW
Retrocopy NLQPALTYWSVFFRFGLCMGFLGPAVSDLCCQTHGSLPQISWVFFSKLFCLLLGSALGGIFKRMLAKSLW

Parental  VLFTSSLTISLVFAVIPFCQNVVVLAI-VIAIAGMAMGFIDTVANMQLVKIYQKDSAVFLQVLHFF-VGF
          .LF.SSLTISLV.AVIPFCQ.VVVLA....A.AG.AMGFI.TVANMQLVKIYQKDSAVFLQVLHFF.VGF
Retrocopy ILFASSLTISLVSAVIPFCQDVVVLAT<ITARAGLAMGFIGTVANMQLVKIYQKDSAVFLQVLHFF>VGF

Parental  GAFLSPLIADPFLSENDCLPTNATNHDRD-SSHFQKILTPHHAQPNLTHHELPA-HAWVGNQMS-YAFWI
          GAFLSPLIADPFLSENDCLPTNAT.HDRD.SSHFQKILT.HHAQPNL.HHELPA.HAWVGN.MS.YAFWI
Retrocopy GAFLSPLIADPFLSENDCLPTNATSHDRDGSSHFQKILTLHHAQPNLSHHELPA<HAWVGNPMSSYAFWI

Parental  MALINLPVPISVLFLLSKERLLPFCPRKKPLLVKTDELALQMELPEKEDSSSPPTKALSETEHGDLFSCC
          MALINLPVPISVLFLL.K.RL...CPRKKPLLVKTDELALQMELPEKEDS...PTKAL.ET.HGDLFS.C
Retrocopy MALINLPVPISVLFLLCKRRLVSCCPRKKPLLVKTDELALQMELPEKEDSPPLPTKALPETGHGDLFSHC

Parental  QKKNFQGASCSFFAIHITAALVLFMTDGI
          QKK.FQG.SCSFFAIHITAALVLFMTDGI
Retrocopy QKKDFQGVSCSFFAIHITAALVLFMTDGI

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	0.33 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	1.18 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_624 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_624 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001804	1 retrocopy	retro_mdom_624 ,