RetrogeneDB ID: retro_mdom_1578

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:36883798..36884371(+)
• 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_1578
GAGGAATATATAAAAAACCTCATTCACAAAACAGAAGATTTAGAAAACACATCCAGGAAAGACAACTTAAAAATCTCTGG
TTTAACTGAAGACCATGACAAAAGAAAAAAGTCTAGATATTATTCCACAGGAAATCATCCAAGAAAACTACTCCAACATT
CTAGAGCAAGAGGAAAAAGTGGACATTGAAAGAATCAACAGTTCACCACCCAACTGAAACACTCAAGAAATTTATAGCCA
AATTCAAGAAGTATCATACCAAGGAAAAAATATTTCAAGCTGCTAAGAAGAAGTCATTCAGATACCATGGAACTACAGTG
AGGATAACACAGGATCTGGCTGCATCTACACTGAAGGACTGAAAGGCATGGAATATGATATTCTGGGAAAGAAGGAGAAC
TAGGTCTAAAACCAAGAATCAAGTCCCCCACAAAATTGACTATATTCTTGCAGGGGAAAGGATAGTAATTTAATAAAAGA
AAATAATTCCAAACATTCATAAAGAAAAGACCATACTTGAACAGAAAATTTGATGCCCAAGCACAGAACTCTAGAGAATT
ATCAAAAGGTAAT

Alignment

ORF - retro_mdom_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.66 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KENMKHLIHKTDDLENRSRRDNLRIIGLPEDHDKRK-SLDIMLQEII-KENFPNILEQEGINTRSHPVLN
          .E..K.LIHKT.DLEN.SR.DNL.I.GL.EDHDKRK.SLDI..QEII.K...P.........T.......
Retrocopy EEYIKNLIHKTEDLENTSRKDNLKISGLTEDHDKRK>SLDIIPQEII>KKTTPTF*SKRKKWTLKESTVH

Parental  PQLTTARNVIAKFKNYQTKEKILQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNIIHTQRKN-CLQP
          ....T....IAKFK.Y.TKEKI.QAAKKKSFRYHGTTVRITQDLAASTLK..KA...I....R....L.P
Retrocopy HPTETLKKFIAKFKKYHTKEKIFQAAKKKSFRYHGTTVRITQDLAASTLKD*KAWNMIFWERRRT>GLKP

Parental  RINYPAKLTIFLQGKVWSFNKIEEFQEFVKKRPHLIRKFDVQAQNSRESSKDN
          RI..P.KLTIFLQGK...FNK...FQ.F.KKRP.L.RKFD.QAQNSRE.SK.N
Retrocopy RIKSPTKLTIFLQGKG**FNKRK*FQTFIKKRPYLNRKFDAQAQNSRELSKGN

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_1578 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1578 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,