RetrogeneDB ID: retro_mdom_1447

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:92903499..92904591(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009035
• Aliases: None
• Description: None

Sequence

>retro_mdom_1447
AGCCCGGGCCCAGGCCCAGATCCCAAACGCAGCGTCCTGGGCCCGGTGGATTTCTCCTCACACTTCTTTCCGTACCTGCT
CTCAATGAAGCAGTTTCTGGATGTCAGATCTGTGAATGCATGAGAAAAGACCTCATTTGTGTTTTTGCAGCATGAGTTGC
CAGTGCTGTTGGCAAACATAATGAAAGAAATAAGTCTTCTTCCAGATAATCTTCTAAGAACACCTTCAGTTCAGCTGGTA
CAGAGCTGGTATATTCATAGTCTACAAGAACGCCTTTATTTTAAAAATAAAAGTGCTGAAGATGCAAAAGCTGTTCATGA
CTTAAGAAAGACTGTCATAAGAATCCGAAATCGACCTAATGATGTCATTCCTACCATGGCTCAGGGTGTGACTGAATACA
AGGAAAGCTTTGTGACTAGCCAGAATCTACAGTATTTTTTGGATTGTTTTTTACAGGAGTCAAATTTCAATCAGAATGCT
ACTCAATCAGCACTCCTTACTATTTGCTGGGAAATGAAAAGGAAGTTCAACTCAGGGAAAACATATTGGAAGCATTAATC
CAAATTGTAATGTCATCGAAGTTTTTAAAGATGGCTATGAAAATGCAAGGCATCTTTGTGATTTTTTTTGTGTTAATTCT
CCAGAACTAGAACTTGAAGAATTAAATGCAAAATCACCAGGATAACCAATGCAAGTGGTTTATGTACCATCACATCTCTA
TCACATGGTGTTTGAACTTTTCAAGAATGCAATGTGGGCAACTATGGAACACCATTTTGACAAAGGTGTTGACCTTCCTT
TTCAGGTTCATATAACACTGGGTAATGGGGATTTGACTGTGAAGATGAGTGATCTGTGAGATGGTGTTCCTTTTAGGAAA
ATTGATAGACTTTTCAACTACATGTATTGAACTGCACCCTGACCTACTCTTCAGACATCTCGAGCTGTGCCCTGGCTGGT
TTTGGTTATGGATTGCCAATATCTCGGCTTTATGCACAGTACTTTCAAGGAGACCTGAAATTGCATTCCTTAGAATGTTA
TGGGACAGATGCTGTTATTTACATTAAGGCCTTATCAACAGTCAGTGGAGAG

Alignment

ORF - retro_mdom_1447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.08 %
• Parental protein coverage: 85.75 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NPGPGAGPERSVPGPVDFYSRFSPSPLSMKQFLDFGSVNACEKTSFMFLRQELPVRLANIMKEISLLPDN
          .PGPG..P.RSV.GPVDF.S.F.P..LSMKQFLD..SVNA.EKTSF.FL..ELPV.LANIMKEISLLPDN
Retrocopy SPGPGPDPKRSVLGPVDFSSHFFPYLLSMKQFLDVRSVNA*EKTSFVFLQHELPVLLANIMKEISLLPDN

Parental  LLRTPSVQLVQSWYIQSLQELLYFKNKSAEDAKAVYDFTDTVIRIRNRHNDVIPTMAQ-CDEYKESFGVD
          LLRTPSVQLVQSWYI.SLQE.LYFKNKSAEDAKAV.D...TVIRIRNR.NDVIPTMAQ...EYKESF...
Retrocopy LLRTPSVQLVQSWYIHSLQERLYFKNKSAEDAKAVHDLRKTVIRIRNRPNDVIPTMAQGVTEYKESF---

Parental  PVTSQNVQYFLDRF-YMSRISIRMLLNQHSLLFGGKGKGSSTHRKHIGSINPNCNVVEVIKDGYENAKRL
          .VTSQN.QYFLD.F.Y.S.ISIRMLLNQHSLLF.GK.KGSST..KHIGSINPNCNV.EV.KDGYENA..L
Retrocopy -VTSQNLQYFLDCF>YRSQISIRMLLNQHSLLFAGK*KGSSTQGKHIGSINPNCNVIEVFKDGYENARHL

Parental  CDLYYVNSPELELEELNAKSPGQPMQVVYVPSHLYHMVFELFKNAMRATMEHHADKGVYPPIQVHVTLGN
          C....VNSPELELEELNAKSPG.PMQVVYVPSHLYHMVFELFKNAM.ATMEHH.DKGV..P.QVH.TLGN
Retrocopy CXXXXVNSPELELEELNAKSPG*PMQVVYVPSHLYHMVFELFKNAMWATMEHHFDKGVDLPFQVHITLGN

Parental  EDLTVKMSDRGGGVPLRKIDRLFNYMYSTAPRPRVETSRAVP-LAGFGYGLPISRLYAQYFQGDLKLYSL
          .DLTVKMSD...GVP.RKIDRLFNYMY.TAP.P...TSRAVP.LAGFGYGLPISRLYAQYFQGDLKL.SL
Retrocopy GDLTVKMSDL*DGVPFRKIDRLFNYMY*TAP*PTLQTSRAVP<LAGFGYGLPISRLYAQYFQGDLKLHSL

Parental  EGYGTDAVIYIKALSTESVE
          E.YGTDAVIYIKALST.S.E
Retrocopy ECYGTDAVIYIKALSTVSGE

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_1447 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1447 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007507	1 retrocopy	retro_cjac_4090,
Cavia porcellus	ENSCPOG00000008434	1 retrocopy	retro_cpor_545,
Macaca mulatta	ENSMMUG00000022553	1 retrocopy	retro_mmul_2511,
Monodelphis domestica	ENSMODG00000001837	1 retrocopy	retro_mdom_1033,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447 ,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509,