RetrogeneDB ID: retro_mdom_631

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:595921379..595922660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012952
• Aliases: None
• Description: None

Sequence

>retro_mdom_631
GGAGTAACATCAGTGAAACCTCCAAGTATAGGAAGCAAACATTTATACAGTAAAGATGCTTACTCTCCAGAGTCATTATC
ACCTGGTACAAATGGCTTCCTGCCTTGGCATACTGCTGAGCGTGACAACAGGTGCAAGGGATTTCCACTGCTTAAAACCC
AAGATTTACCTTGGCCAGTTCAGCAATTAGATTTTCCTGTGAAAGTAATTGTGGAGACCCCATCATGCACAGAAGTGGAA
GAATCAGAAGATGCTGTTTAAGAACCTGTTTCTGAAAAAAAAAATGCCTTAACAGCATACAAGATAAATGAAATACAGGA
AAAATTGGAAGAGTGCATGAAGCAATTAAAAGCAGAAAGGATTATGAGAGTCAAGGCTGATAAACAAGTAACTGAGCTGG
AACTTGAGAATTCCCAATTGTGAAATATAAATTTCTCTCTGTCTGAGGCTCTTTATGCACAATCACTATCAACCATGATT
TTGGAAGATGGTGGTGTTTTGGGCAGTATTGAGTCATCTTTCCAAAAGTTCCATGCTTTTTTGGATCTCCTTAAAGATGC
TGGGCTTGAGCAGCTCGCTACAGTAACTGATATAAATCAGTCAGATTTTAATTTCTTAGATCATCCCCAGATGAACTCTA
CAATTAATGCTTTATTTATAGAAGGAAAGAAAGAACTTGAAGAAAGGCCAGAGTCTAATCAGAACACCCAAGGACCAATG
CAGAGCATCCAAAAAGTTAGTGGAGATTTTAGAGGTTCTTTGCCTCTTGACACCCTCCAGTTTCCACTTTCTACTCTGGA
GGCCTTACCTCCTTCCAAAGAAGTTCAAGAAATTAAGGGCACTGATGATCAGCCAGTTCTTCCTAAAGAATTTGTCTAAA
AATTATCATTTTTAGAAAATATGATTGTTGAAGCTCAAGATCAAAGAAAAGAAGAGGAGACTTTCAGAAGTAGTAGAACT
TCCTCAGAGAAAAGTCCCAGAATGAGTGAACATATCTCAAAACATTCTTCTAAGAAATGGTCTGAAAGTTCTTCTAATTC
CTTCCCTGAGACTCCAGTAAGCCAGAAAAGCAGAGGACACAGGGAGCATACCCCTTCAGATCCTGAAAAATTAAAACATC
CATCTTCAAAAAAATATAGCCTTTCTAGGAAAGAAACTAGAGAAGTAACAGTAATATCTAAGGCAGATAAAAGTAAACAC
AAAACATTAGAACGTTCTAAAAGTGAAACAGTAGTATCTGATCCTGAAATTCCAGAAAGTATTCATTCTCTATCAAGCAC
A

Alignment

ORF - retro_mdom_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 54.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVTSVKPPSIGSKHLYSKDAYSPESLSPGTYGFLPWRTAERANRCRGFPLLKTRDLSWPVQQLDFPVKVT
          GVTSVKPPSIGSKHLYSKDAYSPESLSPGT.GFLPW.TAER.NRC.GFPLLKT.DL.WPVQQLDFPVKV.
Retrocopy GVTSVKPPSIGSKHLYSKDAYSPESLSPGTNGFLPWHTAERDNRCKGFPLLKTQDLPWPVQQLDFPVKVI

Parental  VETPSCSDVEESEDTVLEPVSEKN-ALTPYKINEIQEKLEECIKQLKAERIMRVKADKRVTELELENSQL
          VETPSC..VEESED.V.EPVS....ALT.YKINEIQEKLEEC.KQLKAERIMRVKADK.VTELELENSQL
Retrocopy VETPSCTEVEESEDAV*EPVSXXXXALTAYKINEIQEKLEECMKQLKAERIMRVKADKQVTELELENSQL

Parental  RNINFSLSEALHAQSLATMILEDDGVLGSIESSFQKFHAFLDLLKDAGLGQLATVAGINQSDFNFLDHPQ
          .NINFSLSEAL.AQSL.TMILED.GVLGSIESSFQKFHAFLDLLKDAGL.QLATV..INQSDFNFLDHPQ
Retrocopy *NINFSLSEALYAQSLSTMILEDGGVLGSIESSFQKFHAFLDLLKDAGLEQLATVTDINQSDFNFLDHPQ

Parental  MNSTINALFIEGKKELEERPESNQNTQGPMQSIQKVSGDFRGSLPLGTLQFPVSTLEALPPSKEVQEIKG
          MNSTINALFIEGKKELEERPESNQNTQGPMQSIQKVSGDFRGSLPL.TLQFP.STLEALPPSKEVQEIKG
Retrocopy MNSTINALFIEGKKELEERPESNQNTQGPMQSIQKVSGDFRGSLPLDTLQFPLSTLEALPPSKEVQEIKG

Parental  TDDQPVLPKECVPSPLLSFLENMIVEAQDQRKEEETFRSSRTSSEKSPRMSEHISKHSSKKRSESSSNSF
          TDDQPVLPKE.V....LSFLENMIVEAQDQRKEEETFRSSRTSSEKSPRMSEHISKHSSKK.SESSSNSF
Retrocopy TDDQPVLPKEFV*K--LSFLENMIVEAQDQRKEEETFRSSRTSSEKSPRMSEHISKHSSKKWSESSSNSF

Parental  PETPVSQKSRGHREHTPSDPEKLKHPSSKKCSLSRKETREVTVISKADKSKHKTLERSKSETVVSDPEIP
          PETPVSQKSRGHREHTPSDPEKLKHPSSKK.SLSRKETREVTVISKADKSKHKTLERSKSETVVSDPEIP
Retrocopy PETPVSQKSRGHREHTPSDPEKLKHPSSKKYSLSRKETREVTVISKADKSKHKTLERSKSETVVSDPEIP

Parental  ESIHSLSST
          ESIHSLSST
Retrocopy ESIHSLSST

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	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.79 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_631 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_631 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	ENSMODG00000012952	1 retrocopy	retro_mdom_631 ,