RetrogeneDB ID: retro_mdom_1242

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:65002507..65003173(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000002343
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARRB1
• Ensembl ID: ENSMODG00000007021
• Aliases: None
• Description: arrestin, beta 1 [Source:HGNC Symbol;Acc:711]

Sequence

>retro_mdom_1242
CCCGGGGAGCCGCCCATGGCCGAGACCACTTGTCAGTCTCCGATGTCTGACAAGCCCTTACACTTGGAAACCTCTCTGGA
CAAGGAGATCGACTACCTCGGGGAACCGATCAGTGTCAATGTCCATGTCACCAGCAACAACACCAAAACAGTGAAGAAGA
TAAAAATTCCAGTCCGTCAGTCTGCAGACATCTGCCTGTTCAACATGGCACATTACAAATGCCCCGTGGGTGTGGAGGAG
GCTGATGACATGGTGGCCCCAAGTTCAACATGCTGCAAAGTCTACACCCTCATCCCATTCTTGGCCAACAACTGTGAGAA
GCTAGACCTGGCCCTGGATGGCAAGCTGAAGCATGAAGACACCAACTTGGCTTCCAGTACCCTGTTGAGGGATGGCACAA
ATAAGGAGATCTTAGGAATCATCCTGTCCTACCAAGTCAAAGTGAAGCTGTTTGTTTCCCAAGGAGGCCTGTTGGGAGAT
CTCACATCCAATGATGTGAGGAGGGCTGTTGAACTTCCCTTCACCTTAATGCACCCGAAGCCCAGGGAAGAGCCTTTGTA
TGGAGAAGTTCCAGAGAGTGAAGCGCCCATAGATACCAATCTCATAGAGCTCGATACAAACGATGACGACATTGTCTTTG
AGGACATAGCTCGACAGAGACTGAAA

Alignment

ORF - retro_mdom_1242 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.93 %
• Parental protein coverage: 52.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTA
          PG..P.AETT.Q..MSDKPLHLE.SLDKEI.Y.GEPISVNVHVT.N..KTVKKIKI.VRQ.ADICLFN.A
Retrocopy PGEPPMAETTCQSPMSDKPLHLETSLDKEIDYLGEPISVNVHVTSNNTKTVKKIKIPVRQSADICLFNMA

Parental  QYKCPVAVEEADDMVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLRDGTNKEILGI
          .YKCPV.VEEADDMVAPSST.CKVYTL.PFLANN.EK..LALDGKLKHEDTNLASSTLLRDGTNKEILGI
Retrocopy HYKCPVGVEEADDMVAPSSTCCKVYTLIPFLANNCEKLDLALDGKLKHEDTNLASSTLLRDGTNKEILGI

Parental  IVSYKVKVKLVVSRGGLLGDLASSDV--AVELPFTLMHPKPREEPVRREGDHCMSLLEGTLKQLDHDDDD
          I.SY.VKVKL.VS.GGLLGDL.S.DV..AVELPFTLMHPKPREEP...E...........L..LD..DDD
Retrocopy ILSYQVKVKLFVSQGGLLGDLTSNDVRRAVELPFTLMHPKPREEPLYGEVPESEAPIDTNLIELDTNDDD

Parental  IVFEDFARQRLK
          IVFED.ARQRLK
Retrocopy IVFEDIARQRLK

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_1242 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1242 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
Felis catus	ENSFCAG00000011941	1 retrocopy	retro_fcat_204,
Monodelphis domestica	ENSMODG00000007021	1 retrocopy	retro_mdom_1242 ,