RetrogeneDB ID: retro_mdom_1795

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:135712298..135712832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025406
• Aliases: None
• Description: None

Sequence

>retro_mdom_1795
GATGTAGAAAATCATTCCAAGAGAGACAACTTAAGAATCATTGATCTACCAGAAGTCCATGACAAAAGAAAAAAGCCTGG
ACATCATCCTACAGGAAATTATCCAAGAAAACTGCAGACATTTTAGAACAAGAGGGAAAAGTGGAGATTGAAAGAATCTA
CAGATCACCTCCTGTACCAAATCCCCAACTAACAATAGCCAAATTCAAGAACTATCAGACCAAGGAAAAAATATTATAAG
CTGCTAAGAAGATGTCATTCAGATACCATGGAACTACAATGAGGATAACACAATATCTGGCTGCATCTACACTGAAGGAC
CTAAAGGCATGGCATATGATATTCCGGTAAGCAAGGGAACTAGGTCTAAAACCAAGAATCAACTACCCAGCAAAACTGAC
TATATTCTTACAAGGGTAAGTATGGTCATTTAACAAAATAAAAGAATTCCACATATTTGTAAAGAAAAGACCAGACCTGA
TTAGAAAAATGTGATGCCCAAACAGAGAACCCAAGGGAATCATCAAAAGGTAAT

Alignment

ORF - retro_mdom_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.56 %
• Parental protein coverage: 56.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLENRSRRDNLRIIGLPEDHD-KRKSLDIMLQEIIKENFPNILEQEGINTRSHPVLNPQLTTARNVIAKF
          D.EN.S.RDNLRII.LPE.HD...K................ILEQEG..........P........IAKF
Retrocopy DVENHSKRDNLRIIDLPEVHD<QKKKAWTSSYRKLSKKTADILEQEGKVEIERIYRSPPVPNPQLTIAKF

Parental  KNYQTKEKILQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNIIHTQRKNCLQPRINYPAKLTIFLQG
          KNYQTKEKIL.AAKK.SFRYHGTT.RITQ.LAASTLK..KA...I....R...L.PRINYPAKLTIFLQG
Retrocopy KNYQTKEKIL*AAKKMSFRYHGTTMRITQYLAASTLKDLKAWHMIFR*ARELGLKPRINYPAKLTIFLQG

Parental  KVWSFNKIEEFQEFVKKRPHLIRKF-DVQAQNSRESSKDN
          .VWSFNKI.EF..FVKKRP.LIRK..D.Q..N.RESSK.N
Retrocopy *VWSFNKIKEFHIFVKKRPDLIRKM>DAQTENPRESSKGN

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_1795 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1795 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025406	12 retrocopies	retro_mdom_1000, retro_mdom_1578, retro_mdom_1642, retro_mdom_1712, retro_mdom_1767, retro_mdom_1795 , retro_mdom_2008, retro_mdom_502, retro_mdom_770, retro_mdom_842, retro_mdom_900, retro_mdom_972,