RetrogeneDB ID: retro_mdom_1495

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:13436050..13436500(-)
• Located in intron of: ENSMODG00000018997

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTB
• Ensembl ID: ENSMODG00000005190
• Aliases: None
• Description: clathrin, light chain B [Source:HGNC Symbol;Acc:2091]

Sequence

>retro_mdom_1495
CTCAGCGGAGGGGGAGGAGGGGGGCAGTGCCAGCTGAAGAAGACCTAGCAGCAGCCTTCCTGGCCCAGCAGGAGAGTGAA
AACTATGATGAAGGTTTCGGAGGTGCTGAAGGAGCCCTGCAGCAACCAGTGGCTGAAAATGAGACTGGTATTGTGGACAC
GGGGGACTACAGTCAATGGAGACATGTTCCAAGAAGCCAGTGGTCCTTAAGATGGCTATGCTGCTATGGCCCAGGCAGAT
AGACTGAGTCAGGAACCAGAGAGCATCAGAAAATGGAGAGAGGAGCAGAAGAAATGGCTACAAGAACTGGATACAGCTTT
GAAAGTGACTGAGCAAGAGTGGCGGGAGAAGGCAAAGAAGGATCTGGAAGAATGGAATGTGAGACAGAATGAGCAGATGG
AGAAAAACAAAGTCAGCAACAGAGCATCAGAAGAAGCTTTCCTGAAGGAG

Alignment

ORF - retro_mdom_1495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.52 %
• Parental protein coverage: 68.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFSSGGGPP-VPAEEDPAAAFLAQQESEIAGIENDDEGFGGAEGALQQPAAENGTGIMDMG-TTVNGDMF
          L...GGG...VPA.E...AA....Q.......EN.DEGFGGAEGALQQP.AEN.TGI.D.G.TTVNGDMF
Retrocopy LSGGGGGGQ<VPA-EEDLAAAFLAQQES----ENYDEGFGGAEGALQQPVAENETGIVDTG>TTVNGDMF

Parental  QEANGPSDGYAAVAQADRLSQEPESIRKWREEQKKRLQELDAASKVTEQEWREKAKKDLEEWNVRQNEQM
          QEA.GP.DGYAA.AQADRLSQEPESIRKWREEQKK.LQELD.A.KVTEQEWREKAKKDLEEWNVRQNEQM
Retrocopy QEASGP*DGYAAMAQADRLSQEPESIRKWREEQKKWLQELDTALKVTEQEWREKAKKDLEEWNVRQNEQM

Parental  EKNKVSNRIADKAFYQQ
          EKNKVSNR....AF...
Retrocopy EKNKVSNRASEEAFLKE

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	193.69 RPM
SRP007412_cerebellum	0.00 RPM	255.61 RPM
SRP007412_heart	0.00 RPM	170.84 RPM
SRP007412_kidney	0.00 RPM	36.87 RPM
SRP007412_liver	0.00 RPM	20.14 RPM
SRP007412_testis	0.00 RPM	116.68 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1495 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1495 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	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Monodelphis domestica	ENSMODG00000005190	1 retrocopy	retro_mdom_1495 ,