RetrogeneDB ID: retro_mdom_1782

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:79299021..79299801(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004254
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: B4GALT5
• Ensembl ID: ENSMODG00000016301
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 [Source:HGNC Symbol;Acc:928]

Sequence

>retro_mdom_1782
GCCGCGCTCTTCTTCTTCTCGCTGTCCTCGACCTTTCTGTACTTCGTGTATGTGGCGCCCGGCATAGTGAATACCTACCG
CTTCATGATGCAAGCCCAAGGCATCCTGATCCGAGGCAGCATGAGAACGATAGGAGCTCAGGTGTATGAGCAGGTGGTTC
GGAGTGCGTTTGCCAGGAGGAATAGCAGTGTAAATGACTCAGGTTATCCTCTTGACCTGAATCATAGTGCGACCTTCCTG
CAAACCACAACTTTTCTTCCTGAAGACTTCACATACTTTGCAAACCATACCTGCCCTGAAAGACGCCCTTCTATGAAGGG
TCCAATAGATACAAATAGGAGTGAAATCAGAATGGATGCCATCCATGAATTCTTCTCTAGAGACCCTGCCATCAAGCCTG
AAGGTCATTGGAAGCCCAGGGATTGCATGCCTCCTTGGAAGGTGGCAATTCTTATTCCATTTCGAAACCGATATGAGCAT
CTCCCTGTTTTTTCCGGCATGTGATTCCTATGTTACAACGCCAGCATCTACAGTTTGCATTCTATATTATTGAACCAGCC
GGTACCCAACCCTGCAATCGGGCCATGATCCTTAATGTTGGCTTTCGTGAAGCAACGAGAGACTTGCATTGGGATTGTTT
GATTTTTCACGATGTGGATCATATACCAGAAAATGACCACAACTATTATGGATGTGGGCAAATGCCAAGACATTTTGCCA
CCAAGCTGGATAAGTATATGTATCTGCTTCCTTATAATGAGTTTTTTTGGTGGAGTGAGC

Alignment

ORF - retro_mdom_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.08 %
• Parental protein coverage: 67.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AALFFFSLSSTFLYFVYVAPGIVNTYLFMMQAQGILIRDNMRTIGAQVYEQVVRSAYARRNSSVNDSDYP
          AALFFFSLSSTFLYFVYVAPGIVNTY.FMMQAQGILIR..MRTIGAQVYEQVVRSA.ARRNSSVNDS.YP
Retrocopy AALFFFSLSSTFLYFVYVAPGIVNTYRFMMQAQGILIRGSMRTIGAQVYEQVVRSAFARRNSSVNDSGYP

Parental  LDLNHSETFLQTTTFLPEDFTYFANHTCPERLPSMKGPIDINMSEIRMDDIHEFFSRDPAIKLGGHWKPS
          LDLNHS.TFLQTTTFLPEDFTYFANHTCPER.PSMKGPID.N.SEIRMD.IHEFFSRDPAIK..GHWKP.
Retrocopy LDLNHSATFLQTTTFLPEDFTYFANHTCPERRPSMKGPIDTNRSEIRMDAIHEFFSRDPAIKPEGHWKPR

Parental  DCMPRWKVAILIPFRNRYEHLPV-LFRHLIPMLQRQRLQFAFYVIEQAGTQPFNRAMLFNVGFREAMRDL
          DCMP.WKVAILIPFRNRYEHLPV..FRH.IPMLQRQ.LQFAFY.IE.AGTQP.NRAM..NVGFREA.RDL
Retrocopy DCMPPWKVAILIPFRNRYEHLPV<FFRHVIPMLQRQHLQFAFYIIEPAGTQPCNRAMILNVGFREATRDL

Parental  HWDCLIFHDVDHIPENDRNYYGCGQMPRHFATKLDKYMYLLPYNE-FFGGVS
          HWDCLIFHDVDHIPEND.NYYGCGQMPRHFATKLDKYMYLLPYNE.FFGGVS
Retrocopy HWDCLIFHDVDHIPENDHNYYGCGQMPRHFATKLDKYMYLLPYNE>FFGGVS

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	228.26 RPM
SRP007412_cerebellum	0.00 RPM	133.52 RPM
SRP007412_heart	0.00 RPM	66.58 RPM
SRP007412_kidney	0.00 RPM	133.00 RPM
SRP007412_liver	0.00 RPM	67.47 RPM
SRP007412_testis	0.00 RPM	147.33 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1782 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1782 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016301	1 retrocopy	retro_mdom_1782 ,
Tetraodon nigroviridis	ENSTNIG00000010472	1 retrocopy	retro_tnig_6,
Takifugu rubripes	ENSTRUG00000005726	1 retrocopy	retro_trub_9,
Tursiops truncatus	ENSTTRG00000004300	1 retrocopy	retro_ttru_1533,