RetrogeneDB ID: retro_mdom_32

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:252711330..252712224(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024008
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CDK3
• Ensembl ID: ENSMODG00000007835
• Aliases: None
• Description: cyclin-dependent kinase 3 [Source:HGNC Symbol;Acc:1772]

Sequence

>retro_mdom_32
ATGGAAGACTACACGAAAATAGAAAAAATTGGGGAAGATACCTATGGTGTTGTATATAAGGGTCGACATAAAACTACAGG
CCAGGTGGTAGCCATGAAGAAAATCAGATTAGAGAGTGAAGAAGAGGGTGTTCCAAGTACTGCAATTCGAGAAATTTCTC
TGTTGAAAGAACTTCGTCATCCGAACATTGTCAGCCTTCAAGATGTACTCATGCAAGATGCTAGACTATACCTCATTTTT
GAATTCCTTTCCATGGATCTCAAGAAGTATTTGGATTCTATCCCTCCTGGCCAGTATATGGATTCTTCCCTTGTTAAAAG
TTATTTGTACCAAATATTACAAGGCATTGTCTTTTGTCACTCACGAAGAGTTCTTCACAGAGATTTGAAGCCTCAAAATT
TGTTAATAGATGATAAAGGTGTAATTAAGCTAGCCGACTTTGGACTTGCACGGGCCTTTGGAATACCTATGAGGGTATAT
ACACATGAGGTGGTGACGCTGTGGTACCGGTCTCCGGAGGTGCTGCTCGGCTCGGCCAGGTACTCCACCTCGGTGGACAT
CTGGAGCATCGGCACCATCTTCACTGAACTGGCCACCAAGAAGCCGCTGTTCCACGGAGACTCCGAGATCGACCAGCTCT
TCTGCATCTTCAGGGCTTTGGGGACTCCGAATAACGAAGTGTGGCCGGAAGTGGAGTCGCTGAAGGATTACAAGAACACG
TTCCCTAAGTGGAAGCCAGGCAGTCTGACGTCGCACGTCAAGAACCTAGATGAAAACGGCATCGACCTGCTCTCTAAAAT
GTTGGTCTATGATCCTGCCAAGCGAATTTCTGGCAAAATGGCATTGAACCATCCATATTTTAATGACCTGGACAGTCAGA
TTAAGAAGCTCTAG

Alignment

ORF - retro_mdom_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 95.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVFQKVEKIGEGTYGVVYKARNKQTGQLVALKKIRLDSETEGVPSTAIREISLLKELKHPNIVRLLDVV
          ME...K.EKIGE.TYGVVYK.R.K.TGQ.VA.KKIRL.SE.EGVPSTAIREISLLKEL.HPNIV.L.DV.
Retrocopy MEDYTKIEKIGEDTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVL

Parental  HSEKKLYLVFEFLSQDLKKYMDSAAATE-LPLHLVKSYLFQLLQGVNFCHSHRVIHRDLKPQNLLINELG
          .....LYL.FEFLS.DLKKY.DS..........LVKSYL.Q.LQG..FCHS.RV.HRDLKPQNLLI...G
Retrocopy MQDARLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKG

Parental  AIKLADFGLARAFGVPLRTYTHEVVTLWYRAPEILLGCKFYSTAVDVWSIGCIFAEMVTRRALFPGDSEI
          .IKLADFGLARAFG.P.R.YTHEVVTLWYR.PE.LLG...YST.VD.WSIG.IF.E..T...LF.GDSEI
Retrocopy VIKLADFGLARAFGIPMRVYTHEVVTLWYRSPEVLLGSARYSTSVDIWSIGTIFTELATKKPLFHGDSEI

Parental  DQLFRIFRTLGTPSEATWPGVTQLPDYKGSFPKWTRKSIEEIVPSLDPEGKDLLMQLLQYDPNRRISAKA
          DQLF.IFR.LGTP....WP.V..L.DYK..FPKW...S....V..LD..G.DLL...L.YDP..RIS.K.
Retrocopy DQLFCIFRALGTPNNEVWPEVESLKDYKNTFPKWKPGSLTSHVKNLDENGIDLLSKMLVYDPAKRISGKM

Parental  ALTHHYFSTCKS
          AL.H.YF....S
Retrocopy ALNHPYFNDLDS

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	0.33 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	5.30 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_32 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_32 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000815	4 retrocopies	retro_meug_1371, retro_meug_2186, retro_meug_553, retro_meug_789,
Monodelphis domestica	ENSMODG00000007835	1 retrocopy	retro_mdom_32 ,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,