RetrogeneDB ID: retro_mdom_1746

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:183617792..183619127(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LBR
• Ensembl ID: ENSMODG00000005848
• Aliases: None
• Description: lamin B receptor [Source:HGNC Symbol;Acc:6518]

Sequence

>retro_mdom_1746
AGTTCACTTTATTATGAAGTGGAAGTACTTAGCCAAGATAGCAAATCCCATCTTTACACTGTGAAATACAAAGATGGAAC
TGAACTTGAATTGAAAGAGAGTGATATAAAGCCTTTAACATCATTCAGGCAAAGGAAAAGTGGCTCTTCTTCCAGTTCTC
GTTCCAGACGCCGTGGGAGTCGATCTCACTCTCCTGGCTGTCCGCCCAAAAGCATACGTCGTTCTGCTTTCCAGCATGCA
GAGATTAAAGACGAGAAAGAAATTTTGGAAATCAACTTGTCTCCATTGAAGCAAAGTGGAAACAGCATTAACAGATACAA
TGGTGAACCTGACCGGATAGAAAGGAATGACATCTCTTACAGAAACATTCAGGACAAATCTTATTTGTCACAAGAAAGCA
GCTATCTGGTCACACAGTATAGCCTTCGCCCAAGAAAAGAAGAGATCAAATTTGAAGAAATTATTTCTAGAGAAGAGAGA
AATGTTGCAAAAGAACCAAAATCAATAAGAACTTTTGACATGACATCTACAGAACCAGAGGAATTAGAGTTTGGAGGAGG
GATTGGAGCTTTTTCCATTATGATTGGTCTGCCGGTTATGCTTTTTATGTTATTGTTGATGTGTAAACAGAAAGATCCCA
GTTTTGTGAATCTTCCTCCTCCATTGCCATCTTTGGCTAGTTTATGGGAAACCAGAGTATTTGGAGTTTGTCTGCTTTGG
TTTTTTCTTCAAGCCCTCTTCCATCTACTGCCAATTGGAAAGGTAGTAGAAGGAACACCTCTTTATAGTGGAAGAAGACT
GAAGTATAGATTAAATGGATTCTATGCTTTTATCCTGACATCTGTAGTCATTGGAACATCTTTGTACTGGGGTATAGAGC
TCTATTATGTGTATGACCACTTTCTTCAGTTTGCAGTTGCAGCTACAGTTTTTTCTGTAGCCTTGAGCATTTATCTCTAT
GTGCGGTCCTTGAAAGCATCCAACAATGAGCTCTCTCCAGGAAAATCAGGAAATATCATCTATGATTTCTTTATTGGCCG
TGAATTAAATCCACGAATTGGACATTTTGACCTCAAATATTTCTGTGAATTGCGTCCAGGATTGATTGGTTGGGTTGTTA
TTAATTTAATAATGCTTTTGGCAGAGATGAAGGTCCAAGGTCGTGACACCCCGTCTTTAGCAATGATATTGGTTAACAGT
TTCCAGCTTTTATATGTTGTGGATGCTCTTTGGCATGAGGAGGCTTTGCTGACAACAATGGACATTATGCATGATGGATT
TGGGTTCATGTTGGCATTTGGAGATTTGGTATGGGTGCCATTTGTTTATAGTCTA

Alignment

ORF - retro_mdom_1746 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98. %
• Parental protein coverage: 73.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSLYYEVEVLSQDSKSHLYTVKYKDGTELELKESDIKPLTSFRQRKSGSSSSSPSRRRGSRSRSRSRSPG
          SSLYYEVEVLSQDSKSHLYTVKYKDGTELELKESDIKPLTSFRQRKSGSSSSS.SRRRG....SRS.SPG
Retrocopy SSLYYEVEVLSQDSKSHLYTVKYKDGTELELKESDIKPLTSFRQRKSGSSSSSRSRRRG----SRSHSPG

Parental  RPPKSIRRSASQHAEIKDKKEILEINLSPLKQSGNSINRYNGEPDRIERNDISYRNIQDKSYLSQESSYL
          .PPKSIRRSA.QHAEIKD.KEILEINLSPLKQSGNSINRYNGEPDRIERNDISYRNIQDKSYLSQESSYL
Retrocopy CPPKSIRRSAFQHAEIKDEKEILEINLSPLKQSGNSINRYNGEPDRIERNDISYRNIQDKSYLSQESSYL

Parental  VTQYSLRPRKEEIKFEEIISREERNVAKEPKSIRTFDMTSTEPEELEFGGGIGAFSIMIGLPVMLFMLLL
          VTQYSLRPRKEEIKFEEIISREERNVAKEPKSIRTFDMTSTEPEELEFGGGIGAFSIMIGLPVMLFMLLL
Retrocopy VTQYSLRPRKEEIKFEEIISREERNVAKEPKSIRTFDMTSTEPEELEFGGGIGAFSIMIGLPVMLFMLLL

Parental  MCKQKDPSFVNLPPPLPSLASLWETRVFGVCLLWFFLQALFHLLPIGKVVEGTPLYSGRRLKYRLNGFYA
          MCKQKDPSFVNLPPPLPSLASLWETRVFGVCLLWFFLQALFHLLPIGKVVEGTPLYSGRRLKYRLNGFYA
Retrocopy MCKQKDPSFVNLPPPLPSLASLWETRVFGVCLLWFFLQALFHLLPIGKVVEGTPLYSGRRLKYRLNGFYA

Parental  FILTSVVIGTSLYWGIELYYVYDHFLQFAVAATVFSVALSIYLYVRSLKASNNELSPGKSGNIIYDFFIG
          FILTSVVIGTSLYWGIELYYVYDHFLQFAVAATVFSVALSIYLYVRSLKASNNELSPGKSGNIIYDFFIG
Retrocopy FILTSVVIGTSLYWGIELYYVYDHFLQFAVAATVFSVALSIYLYVRSLKASNNELSPGKSGNIIYDFFIG

Parental  RELNPRIGHFDLKYFCELRPGLIGWVVINLIMLLAEMKVQGRDTPSLAMILVNSFQLLYVVDALWHEEAL
          RELNPRIGHFDLKYFCELRPGLIGWVVINLIMLLAEMKVQGRDTPSLAMILVNSFQLLYVVDALWHEEAL
Retrocopy RELNPRIGHFDLKYFCELRPGLIGWVVINLIMLLAEMKVQGRDTPSLAMILVNSFQLLYVVDALWHEEAL

Parental  LTTMDIMHDGFGFMLAFGDLVWVPFVYSL
          LTTMDIMHDGFGFMLAFGDLVWVPFVYSL
Retrocopy LTTMDIMHDGFGFMLAFGDLVWVPFVYSL

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_1746 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1746 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005848	1 retrocopy	retro_mdom_1746 ,
Oryctolagus cuniculus	ENSOCUG00000000285	1 retrocopy	retro_ocun_963,