RetrogeneDB ID: retro_mdom_1154

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:265528276..265528704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2A2
• Ensembl ID: ENSMODG00000028436
• Aliases: None
• Description: adaptor-related protein complex 2, alpha 2 subunit [Source:HGNC Symbol;Acc:562]

Sequence

>retro_mdom_1154
AACCTGCTCAGCTCCAACCAGTACACAGAGAAGCAGACTGGGTACCTTTTCATCTCTGTCCTCGTGAACTCCAACAGCGA
GCTCATTTGCCTGATCAAGAATGGCCTGGCAAGCCGGAACCCCACCTTCATGGGCCTGGCTCTGGACTGCATCGCCAACG
TGGGCAGCCAGGAGATGGCCGAAGCCTTTGCTGGAGAAATCCCCAAAATCCTCGTGGCTTGAGATACCATGGATAGTGTC
AACCTGAGTGGGGCCCTGTGCTTGCTGCGCTAGTATAGAACGTCCCGGGACCTCATGCCCACGGGCAACTGGACTTCTCC
TGTTGTGCACCTCTCAACGACCAGCACCTGGGTGTCGTGACTGCCGCCACCAGCCTCATCACCACGCTGGCCCAGAAGAA
CCCAGAAGACTTCAAGATATCTAGTTCA

Alignment

ORF - retro_mdom_1154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 68.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGE
          NLLSSN.YTEKQ.GYLFISVLVNSNSELI.L....IKN.LASRNPTFMGLAL.CIANVGS.EMAEAFAGE
Retrocopy NLLSSNQYTEKQTGYLFISVLVNSNSELICL----IKNGLASRNPTFMGLALDCIANVGSQEMAEAFAGE

Parental  IPKILVAGDTMDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHL-LNDQHLGVVTAATSLITTLAQKNP
          IPKILVA.DTMDSV..S.ALCLLR.YRTS.DL.P.G.WTS.VVHL.LNDQHLGVVTAATSLITTLAQKNP
Retrocopy IPKILVA*DTMDSVNLSGALCLLR*YRTSRDLMPTGNWTSPVVHL<LNDQHLGVVTAATSLITTLAQKNP

Parental  EEFKTSVS
          E.FK.S.S
Retrocopy EDFKISSS

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_1154 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1154 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	ENSMODG00000028436	1 retrocopy	retro_mdom_1154 ,