RetrogeneDB ID: retro_mdom_1362

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:142639918..142640698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002633
• Aliases: None
• Description: None

Sequence

>retro_mdom_1362
GAAACAGAGGCACTTGAAATAAAATAAGAAAATAGTGTCTTGAAAGCCAAAATCAACCAGCTTGAAAATGAGGCAAAGGA
GATGAAAGATGACCTCCAAAGAAAATCAGACCAGAAGGAGAAGGATGACCAAAAAGCCAGGGAAGAAATCTAATCTTTAA
TATCTAGAATAAAACAACTAGAAGCACCAATTTCACAAGGCAGTAGGACACTATAAAACAAAACCAAAAGAATGAAAATA
AAATTGAGGAAAATATGAAGTACCTCATTAACAAAACAAAAGATTTAGAATATTGTTACAGGAGAGATAACTTAAGAATC
ATTGGTAAACCAGAAGACCATGACAAAAGGAAAAACCTGGACACATACTACAGGAAATTATACAAGAAAACTGCCCTGTT
ATTCTAGAACAAGAAGGAAAAGTGGAGAGTACTTAATCCCCAACTGACAACACCCAGAAATGGTATAGTCAAATTCAAGA
ACTATCAGACCAAGGAAAAAAATATTCCAAGCTTCTAAGAGGTCATTCAGGTACCATGTAACCACAGTGAGGAAAACACA
GGATCTGGCTGCATCTACACTGAATGACCAAAAGGCATGGAATATGATATTCTGGGACCTAGGTCTACAACCAAGAATCA
ATTACGCAGCAAAACTGACCATATTTTTATAAGGGAAAGTATGGACATTTAACAAAATAGAAGAATTCCAAGCATCTGTA
AAGAAAAGGCCAGATTTGAACAGAAAATATGATGCCCAAGCAGAGAATTAAAGAGAATCA

Alignment

ORF - retro_mdom_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EKQKQSLKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEA-SDFTRHQ
          E......K.....L..K....E...........R.SDQKEKDD.KAR.EI.S...RI.QLEA...FTR..
Retrocopy ETEALEIK*ENSVLKAKINQLENEAKEMKDDLQRKSDQKEKDDQKAREEI*SLISRIKQLEA<TNFTRQ*

Parental  HTIKQNQKNKI-IEENMKHLIHKTEDLENRSRRDNLRIIGLLEDYDKRKSLDI-ILQEIIQENCPDITEQ
          .TIKQNQKN...IEENMK.LI.KT.DLE...RRDNLRIIG..ED.DKRK.LD..ILQEIIQENCP.I.EQ
Retrocopy DTIKQNQKNENKIEENMKYLINKTKDLEYCYRRDNLRIIGKPEDHDKRKNLDT<ILQEIIQENCPVILEQ

Parental  EGKVE-IERIHRSTHRNVLAKFKKSQTKEK-ILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIFW
          EGKVE........T.RN...KFK..QTKEK.I.Q..K..SFR.H.T.VR.TQDL.ASTL.D..AWNMIFW
Retrocopy EGKVE>VLNPQLTTPRNGIVKFKNYQTKEK>IFQASKR-SFRYHVTTVRKTQDLAASTLNDQKAWNMIFW

Parental  KARELGLQPRIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQNSRES
          ....LGLQPRI.Y.AKLTIFL.GKVW.FNKIE.FQA.VKKRPD.NRK.DA.A.N.RES
Retrocopy ---DLGLQPRINYAAKLTIFL*GKVWTFNKIEEFQASVKKRPDLNRKYDAQAEN*RES

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_1362 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1362 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002633	6 retrocopies	retro_mdom_1009, retro_mdom_1362 , retro_mdom_1477, retro_mdom_1723, retro_mdom_1764, retro_mdom_329,