RetrogeneDB ID: retro_mdom_1772

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:50370622..50371248(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSMODG00000017889
• Aliases: None
• Description: synaptosomal-associated protein, 23kDa [Source:HGNC Symbol;Acc:11131]

Sequence

>retro_mdom_1772
GATAATCTATCAGCAGAAGAAATTCAGGTAAGGGCGCACCAGGTGACAGATGGGTCCCTAGAAAGTACAAGGAGAATCCT
GGGTTTAGCAATTGAGTCTCAGGATGCAGGAATCAAAACCATCACTATGCTGGATGAACAAGGGGAAAAACTGAACCGCA
TAGAAGAAAGCATGGACCAAATAAATAAAGACATGAGAGAAGCAGAGAAGATGTTAACAGAATTCAACAAATGTTGCAGC
CTTTGTGTTTGCCCTTGGAATAGGTCAGCAAATTTTGAGTCTGGCAAGGCCTATAAAGCAACATGGGCTGAAGGTGGAGA
CAGTTCACCTGGTAATGTGGTTTCTAAGCAGCCAGGCCATATGACAAATGGTCAACCTCAGCAAACAGCTGCAGGAGGAG
CCAGTGGTGGATATATTAAACAGATAACTAATGATGCCAGAGAAGATGAAATGGAAGAAAATTTGACTCAGGTGGACAGT
ATCTTGGGGAACTTGAAAACAATGGCCTTAGACATGGACAATGAGATTGACTCTCAGAACAAATAGGGAGAATTACTGAG
AAGGCTGATACTAACAAAAATCGTATTGATCTTGCCAATGCCAAAGCAAAGAAACTCATTGATAGT

Alignment

ORF - retro_mdom_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.0 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DNLSAEEIQLRAHQVTDESLESTRRILGLAIESQDAGIKTITMLDEQGEKLNRIEEGMDQINKDMREAEK
          DNLSAEEIQ.RAHQVTD.SLESTRRILGLAIESQDAGIKTITMLDEQGEKLNRIEE.MDQINKDMREAEK
Retrocopy DNLSAEEIQVRAHQVTDGSLESTRRILGLAIESQDAGIKTITMLDEQGEKLNRIEESMDQINKDMREAEK

Parental  TLTELNKCCGLCVCPWNRSANFESGKAYKATWAEGGDSSPGNVVSKQPGRMTNGQPQQTAAGGASGGYIK
          .LTE.NKCC.LCVCPWNRSANFESGKAYKATWAEGGDSSPGNVVSKQPG.MTNGQPQQTAAGGASGGYIK
Retrocopy MLTEFNKCCSLCVCPWNRSANFESGKAYKATWAEGGDSSPGNVVSKQPGHMTNGQPQQTAAGGASGGYIK

Parental  RITNDAREDEMEENLTQVGSILGNLKTMALDMGNEIDSQNKQIGRIIEK-ADTNKDRIDLANAKAKKLID
          .ITNDAREDEMEENLTQV.SILGNLKTMALDM.NEIDSQNK..G......ADTNK.RIDLANAKAKKLID
Retrocopy QITNDAREDEMEENLTQVDSILGNLKTMALDMDNEIDSQNK-*GELLRR<ADTNKNRIDLANAKAKKLID

Parental  S
          S
Retrocopy S

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	12.28 RPM
SRP007412_cerebellum	0.00 RPM	10.45 RPM
SRP007412_heart	0.00 RPM	60.00 RPM
SRP007412_kidney	0.00 RPM	126.42 RPM
SRP007412_liver	0.00 RPM	74.52 RPM
SRP007412_testis	0.00 RPM	107.25 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1772 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1772 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772 ,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,