RetrogeneDB ID: retro_mdom_1084

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:37328900..37329457(-)
• Located in intron of: ENSMODG00000019728

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021479
• Aliases: None
• Description: None

Sequence

>retro_mdom_1084
GATGCCAATGGGTTGTGTGAGTTTTTGGACAACTTGGGCTTCACTCACAGAGAAGAAGGAGATTTGGGACAGGGTATGGC
TTCCAGTGGAGACATTTTGGGGCAGAATACAGAGAGATGAACACAGATTATTCTGGGCAAGGAGTGGATCAGCTACAAAG
TCACTGACAAAATCAAAACCAACCCTGATGACAGAAGGATCATTATGTGCGCTTAGAATCCAAAAGATCTTCCTCTCATG
GCCTTGCCTCCATGCCAGCTCTCTGTCCGTTCTACGTAGTGAACGGAGAGCTTTCCTGTCAACTATACCAGCAATCTGGA
GATATGGGCATCGGGGTGCCGTTCAGCATTGCCAGTTACTTCCTGCTCACCTACATGATCACTCACACCACGGGCCTGAA
GCCAGGTGACTTTGTACCTTCTCTGGGAGATGCTCATGTATATGTGAATCATATTGAGTCCCTAAAAATTCAGCTTCCAT
GAGAGCAAAGACCTTTCCCCAAGCTCAAAATTCTTCAGAAAGTGGAAATCTTTGACAACTTCCTGATTGAAGGTTAC

Alignment

ORF - retro_mdom_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 55.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DANGSREFLDNLGLTQREEGDLGPV-YGFQWRHFGAEYKEMNTDYSGQGVDQLQ-KVIDKIK-TNPDDRR
          DANG..EFLDNLG.T.REEGDLG...YGFQWRHFGAEY.EMNTDYSGQGVDQLQ.K...K.K.TNPDDRR
Retrocopy DANGLCEFLDNLGFTHREEGDLGQG<YGFQWRHFGAEYREMNTDYSGQGVDQLQ<KSLTKSK<TNPDDRR

Parental  LIMCAWNPKDLPLMALPPCH-ALCQFYVANGELSCQLYQRSGDMGLGVPFNIASYSLLTYMIAHITGLKP
          .IMCA.NPKDLPLMALPPC..ALC.FYV.NGELSCQLYQ.SGDMG.GVPF.IASY.LLTYMI.H.TGLKP
Retrocopy IIMCA*NPKDLPLMALPPCQ<ALCPFYVVNGELSCQLYQQSGDMGIGVPFSIASYFLLTYMITHTTGLKP

Parental  GDFVHSLGDAHVYMNHIEPLKIQLQREPRPFPKLKILRKVESIDDFKAEDF
          GDFV.SLGDAHVY.NHIE.LKIQL..E.RPFPKLKIL.KVE..D.F..E..
Retrocopy GDFVPSLGDAHVYVNHIESLKIQLP*EQRPFPKLKILQKVEIFDNFLIEGY

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_1084 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1084 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084 , retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,