RetrogeneDB ID: retro_mdom_1931

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:184506307..184507416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAU1
• Ensembl ID: ENSMODG00000016276
• Aliases: None
• Description: staufen double-stranded RNA binding protein 1 [Source:HGNC Symbol;Acc:11370]

Sequence

>retro_mdom_1931
CAGGTCTCCAGGGAGAGTGGCCCACCTCACATGAAGACTTTTGTGACAAAGGTGTCAGTTGGTGAATTCATGGGTGAAGG
TGAAAGAAAAAGCAAGAAGATTTCAAAGAAAAATGGTGCTATAGCTGTCCTTGAGGGACTAAAGAAATTACCTCCTCTTC
GAAAAGTTGAGAAAATGAAGCCACAAATTAAAAAGAAAACAAAATCTATAGTTAAGCTACCAAATATGGTCAAGGAATGA
ATCCAATTATCCAACTTGCCCAGATCCAACAGGTCAAAAAAGATAAGGAGCCTGAATACATGCTTCTCACTGAGCGAGGT
CTTCCTCATCGCAGGGAGTTTGTGAGGCAGGTCAAAGTTGGTGGCCATACTGCTGAAGGAATGGGCATGAATAAGAAGGT
AGAAAAGCGCAATGCAGCTGAAAATATGTTAGAGATCCTAGGCTTCAAAGGCCCCCCAAGCCCAGCCCCCTAATCCAGCA
GTGAAGACAGAAGAAAAAACCCCAGTAAAGGTGATAGAAGACAAGTTATCTTTTTTGAGCCCAACTCTGGTGATGAAAAT
GTGACCCGTAATAAGAAAGATGAAATTAGGATGCCTTATCTCAGTCATCAGCAACTTTCAGCAGGAATTCTTCCCGTGGT
GCCTGAAGTGGCACAGGCTGTAGGAGTCAAGCAAGGACATCATACCAAAAAGTTTATCAAGTTAGCTCTGAATCCTGCCA
AGGCATCTATCACAGCCATGATTGCTAGAGAGCTATTGTATGGGGGGACCTCCCCAACAGCTGAGACCATTTTAAAGAAT
AACATCTCCTCAGGCCATGTCTCCCACAGGCCACTTACTGGACCCTCTGAACAACTGGATTATCTTTCCAATGTCCAGGG
AATACAGGTGGAATACAAAGACTTTCCAAAAAACAACAAGAATGAGTTTGTCTCTCTTATAAATTGTTCCTCTCAGCTAT
GTCTGATCAGCCATGGAATTGGAAAGTATGTGGCATCCTGCCATGACATGGCTGCATTGAACATTTTAAAGTTGCTGTCT
GAGGTGGACCAACAAAGTCCAGAGATGCCAAGAACATAAAATGGACCAATGTCTGTGTGTGGGAGGTGC

Alignment

ORF - retro_mdom_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 56.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVTRESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELKKLPPLPTVEKMKPRIKKKTKSI
          .V.RESGPPHMK.FVTKVSVGEFMGEGE.KSKKISKKN.AIAVLE.LKK...LP...K.........K..
Retrocopy QVSRESGPPHMKTFVTKVSVGEFMGEGERKSKKISKKNGAIAVLEGLKK---LPPLRKVEKMKPQIKKKT

Parental  VKLQTSP-EYGQGMNPISRLAQIQQAKKDKEPEYMLLTERGLPRRREFVMQVKVGGHTAEGMGTNKKVAK
          ......P..YGQGMNPI..LAQIQQ.KKDKEPEYMLLTERGLP.RREFV.QVKVGGHTAEGMG.NKKV.K
Retrocopy KSIVKLP<KYGQGMNPIIQLAQIQQVKKDKEPEYMLLTERGLPHRREFVRQVKVGGHTAEGMGMNKKVEK

Parental  RNAAENMLEILGFK-VPQAQPPKPALKTEEKT-PVKKPGDGRKVTFFEPNSGDENVTSNKEDEFRMPYLS
          RNAAENMLEILGFK..PQAQPP.PA.KTEEKT.P.K..GD.R.V.FFEPNSGDENVT.NK.DE.RMPYLS
Retrocopy RNAAENMLEILGFK>APQAQPPNPAVKTEEKT<PSK--GDRRQVIFFEPNSGDENVTRNKKDEIRMPYLS

Parental  HQQLPAGILPMVPEVAQAVGVNQGHHTKEFTRVAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSG
          HQQL.AGILP.VPEVAQAVGV.QGHHTK.F...A.NPAKA..TAMIARELLYGGTSPTAETILKNNISSG
Retrocopy HQQLSAGILPVVPEVAQAVGVKQGHHTKKFIKLALNPAKASITAMIARELLYGGTSPTAETILKNNISSG

Parental  HVPHGPLTRPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNI
          HV.H.PLT.PSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQ..LISHGIGK.V.SCHDMAALNI
Retrocopy HVSHRPLTGPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQLCLISHGIGKYVASCHDMAALNI

Parental  LKLLSELDQQSTEMPRTGNGPMSVCGRC
          LKLLSE.DQQS.EMPRT.NGPMSVCGRC
Retrocopy LKLLSEVDQQSPEMPRT*NGPMSVCGRC

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	631.86 RPM
SRP007412_cerebellum	0.00 RPM	678.37 RPM
SRP007412_heart	0.00 RPM	607.23 RPM
SRP007412_kidney	0.00 RPM	812.49 RPM
SRP007412_liver	0.00 RPM	504.50 RPM
SRP007412_testis	0.00 RPM	328.44 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1931 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1931 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016233	1 retrocopy	retro_cjac_4102,
Monodelphis domestica	ENSMODG00000016276	1 retrocopy	retro_mdom_1931 ,
Sus scrofa	ENSSSCG00000027444	1 retrocopy	retro_sscr_233,