RetrogeneDB ID: retro_mdom_113

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:467804339..467805410(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023294
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017503
• Aliases: None
• Description: None

Sequence

>retro_mdom_113
CTTTTATTAGCAGCCACTATAATTGGACTCCTAGCCTGTTTCCTTCATTTTTTCCGACCCTTAAACTGCATCTTGATGAG
GAATCATGAGGTTGTCCAGCAACCAAAGTCTTACGACAATCTCACCCAGAGATTGACCAGGGAAGCACTCAAGTTCATAA
ACAGGAACACCAGGACACCCTTCCTTCTTTTCTTATCCTATATTCATGTCCACACTGCACTTTTTTCCTCTAAGGAGTTT
GTGGGCAAGAGCAAACATGGAATATATGGGGATGCTGTGGAGGAGATGGATTGGAGTATAGGGCAGATCTTAAAAACTCT
AGATAAGAAGAAATTGACAAATAAGACACTTGTGTACTTTACCTCTGACCAAGGAGCTCACATCGAGGAGGTAACCGACA
AGGGAGACATCCATGGAGGAAGTAATGGAATTTATAAAGGGGGAAAAGCTAATAACTGGGAAGAAGGGATCCGGGTTCCA
GGACTTCTTCGCTGGCCTGGAGTGCTACAGCTTGGAACAGTGATTGATGAACCAACTAGTAACATGGATTTGTTCCTGAC
CATTGTCAAACTTGCAGGAGCAGCATTGCCTGAGGACAGAGTTATTGATGGACATGATCTGATGCCCTTGCTTCAAGGAA
AAATTCTCCAATCTGAGCATGAATTTCTTTTCCATTACTGTAATACATATTTAAATGCAGTGCACTGGCATCCGAGAAAC
AGCACATCTATCTGGAAAGCTTTTTTCTTTACACCAAAGTTTAAGCCAGATGATTACAATGGCTGTTTTCCAACCCACGT
GTGCTTTTGCAATGGGCATTATGTCACTTGTCATAATCCATCCCTACTCTTTGACATCTCCAAACACCCAAAAGAGAGAC
ATCCATTAACTTCAAAAATGGAAAACCATTTTCATGAAAGTCTGAGAGTCATGCAAGAAGCAGCGGACAACCATATGAAG
ACACTCAGTGCAGTTCCCAATCAGTTATCTTGGGGAAACTTTCTTTGGAAATCCTGGCTTCAGTTGTGTTGTTCTTCTTC
TTATCTCTCCTGCCATTGTGATCGGGAAGCC

Alignment

ORF - retro_mdom_113 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 60.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAATIIGLLACFLHFFRPLNCILMRNHEVVQQPMSYDNLTQRLTREALKFINRNTGTPFLLFLSYIHV
          LLLAATIIGLLACFLHFFRPLNCILMRNHEVVQQP.SYDNLTQRLTREALKFINRNT.TPFLLFLSYIHV
Retrocopy LLLAATIIGLLACFLHFFRPLNCILMRNHEVVQQPKSYDNLTQRLTREALKFINRNTRTPFLLFLSYIHV

Parental  HTALFSSKEFVGKSKHGIYGDAVEEMDWSIGQILKALDKKKLTNKTLVYFTSDQGAHIEEVTDKGDIHGG
          HTALFSSKEFVGKSKHGIYGDAVEEMDWSIGQILK.LDKKKLTNKTLVYFTSDQGAHIEEVTDKGDIHGG
Retrocopy HTALFSSKEFVGKSKHGIYGDAVEEMDWSIGQILKTLDKKKLTNKTLVYFTSDQGAHIEEVTDKGDIHGG

Parental  SNGIYKGGKANNWEGGIRVPGLLRWPGVLQPGTVIDEPTSNMDLFPTIVKLAGAALPEDRVIDGRDLMPL
          SNGIYKGGKANNWE.GIRVPGLLRWPGVLQ.GTVIDEPTSNMDLF.TIVKLAGAALPEDRVIDG.DLMPL
Retrocopy SNGIYKGGKANNWEEGIRVPGLLRWPGVLQLGTVIDEPTSNMDLFLTIVKLAGAALPEDRVIDGHDLMPL

Parental  LQGKILQSEHEFLFHYCNAYLNAVRWHPRNSTSIWKAFFFTPKFKPDDSNGCFPTHVCFCNGHYVTRHNP
          LQGKILQSEHEFLFHYCN.YLNAV.WHPRNSTSIWKAFFFTPKFKPDD.NGCFPTHVCFCNGHYVT.HNP
Retrocopy LQGKILQSEHEFLFHYCNTYLNAVHWHPRNSTSIWKAFFFTPKFKPDDYNGCFPTHVCFCNGHYVTCHNP

Parental  PLLFDISKDPKERHPLTSKTENHFHEILRVMQEAADNHTKTLSAVPNQLSWGNLLWKPWLQLCCSSSYLS
          .LLFDISK.PKERHPLTSK.ENHFHE.LRVMQEAADNH.KTLSAVPNQLSWGN.LWK.WLQLCCSSSYLS
Retrocopy SLLFDISKHPKERHPLTSKMENHFHESLRVMQEAADNHMKTLSAVPNQLSWGNFLWKSWLQLCCSSSYLS

Parental  CHCDREA
          CHCDREA
Retrocopy CHCDREA

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	0.12 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	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_113 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_113 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017503	1 retrocopy	retro_mdom_113 ,