RetrogeneDB ID: retro_mdom_1516

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:94541766..94542515(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLK14
• Ensembl ID: ENSMODG00000020815
• Aliases: None
• Description: kallikrein-related peptidase 14 [Source:HGNC Symbol;Acc:6362]

Sequence

>retro_mdom_1516
ATGTTGCTCCTGGTCTCCTCATTGCTTCTTCTGTTGCCCCCCACCAGTGTCCAGAGGTATGGGGACAAGATCATTGGTGG
CTACACTTGTATCCCACTCCCAGCCCTGGAAGGCTATGATGTTCATCTTTCAAAGGTTCCACTATGGAGGTGTCTTGCTG
TCCAAATGATGGGTCCTCACAGCAGCTTGCTGTGGCCACTAGAACCTTCGAGTGGCCTGGGGGAACACAACCTCCAATGC
CTGGAGCCCTCGCAGCAAATACTCAGGGTGGACCATGGGGTAGTCTACTCCAGGTACAACTATAGAACCAATGATCATGA
CCTCATGCTGCTCCACCTAGAGAGGCCAGTGAAGCTGCTCCGAGAGATCCAACCCATTCAGGGTCAAGAAACTGTGCCAG
TCCTGGGACCAACTGTCTGGTGTCAGGCTGGGGCACTATTTCCAGTCCTAATGCCAGATATTCCAGCTCCCTCCAGTGTG
TGAACATCAACATCTTATCCGATGAAAGCTGCAGAAATGCCTACCCAGGAACCATCACTGGAGGCATGCTCTGTGCCAGG
TACCAGAAAGGGGGAAAGGATTTCTGCCAGGGTGACTTCAGTGACCCCTTGGTGTACAATGGGGCTCTGTAGGGTCTGGT
GTCTTGGGGCAGTGAACACTGTGCCCAAGCCAGGTATCCCGGCATCTATACCAAGCTATGTAGTTACTGGACCTGGATCG
AAAATGAAATGTGGAAGAGGCAGAAACAC

Alignment

ORF - retro_mdom_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLLLVSSLLLLLA-PAVAQRDGDKIIGGYTCIPHSQPWQAALFASRKFHCGGVLLSNRWVLTAAHCGHWN
          MLLLVSSLLLLL..P.V....G.......T...HSQPW.A..F....FH.GGVLLS..WVLTAA.CGH.N
Retrocopy MLLLVSSLLLLLP>PPVSRGMGTRSLVA-TLVSHSQPWKAMMFIFQRFHYGGVLLSK*WVLTAACCGH*N

Parental  LRVA-LGKHNLQRLEPSQQMLRVNRQVVYPRYNQRTNDHDLMLLHLERPVKLTREIQPIQV-ARNCASPG
          LRVA.LG.HNLQ.LEPSQQ.LRV...VVY.RYN.RTNDHDLMLLHLERPVKL.REIQPIQ...RNCASPG
Retrocopy LRVA<LGEHNLQCLEPSQQILRVDHGVVYSRYNYRTNDHDLMLLHLERPVKLLREIQPIQG<SRNCASPG

Parental  TSCLVSGWGTISSPHVRYPSTLQCVNIDILSDERCRNSYPGAITRGMVCAGDQKGEKDSCQGDSGGPLVC
          T.CLVSGWGTISSP..RY.S.LQCVNI.ILSDE.CRN.YPG.IT.GM.CA..QKG.KD.CQGD...PLV.
Retrocopy TNCLVSGWGTISSPNARYSSSLQCVNINILSDESCRNAYPGTITGGMLCARYQKGGKDFCQGDFSDPLVY

Parental  NGALQGLVSWGSEQCAQAKYPGVYTNLCRYWTWIQNEVRKRQKH
          NGAL.GLVSWGSE.CAQA.YPG.YT.LC.YWTWI.NE..KRQKH
Retrocopy NGAL*GLVSWGSEHCAQARYPGIYTKLCSYWTWIENEMWKRQKH

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_1516 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1516 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001969	7 retrocopies	retro_meug_1025, retro_meug_1028, retro_meug_1038, retro_meug_1108, retro_meug_1959, retro_meug_2018, retro_meug_707,
Monodelphis domestica	ENSMODG00000020815	1 retrocopy	retro_mdom_1516 ,