RetrogeneDB ID: retro_mdom_1378

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:198276474..198277130(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC43
• Ensembl ID: ENSMODG00000011411
• Aliases: None
• Description: coiled-coil domain containing 43 [Source:HGNC Symbol;Acc:26472]

Sequence

>retro_mdom_1378
ATGGTGGTGCCCAGCAGAGCCATGGCTTTGGGTGAACTCAATGGAAGCTTTGAGTGGTGGCTGGACAGATGGCTGGAGGC
ATTGGGGGTAGACACAGCCCAGCATGGCACCAACATTCAAGGTGTCCTGCAGGAAGACATTGAGTGGGAGAGGCTATATG
TGCTATAGGTCATCCTTATCCCCTTCCTTGAAGGAGACTCATTCCTTGATATCTACAGAGAGATTGTGGAGTGGTGGTCA
GAATCCAGAATGTTGTCACAAAACAGAAAAACAAAAGATTAATTTCAAGCCATCACCACCGTTACTGATAAGAGGGTGCA
GATTGTGGTGAAACCCAAGATAGCTTCAGAGAAGAAGCAGTGGAAAGCTATCTATTGACCCAGTATGCCAATGTGACAGA
TGTGGAGGATGAAGCAGATCAGAAGGATGGTTCAGTTGCTACAACAGTGCTAGTGAATACTGTGTCTGAAAAAAATCTCT
CTTCTGAAACACATGTGGAAGATGTCCTGAATGCTTGAAAATTGAAGGGAGCTTCACTGAGGGATGAGTCTCAGAGGAAG
AAGAAACAGGACAAACTACAAAGAGAAAAAGATAATCTGTCCAAACAGGAACGAAAGGAGAAGGAGAAGAAAAGGACACA
GAAAAGAGAGTGCAAA

Alignment

ORF - retro_mdom_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPSGATASGEGDGGFGPWLDGRLEALGVDRAVYGAYIRGVLQEDEEEERLDALQGILAAFLEEDSLLD
          M..PS.A.A.GE..G.F..WLD..LEALGVD.A..G..I.GVLQED.E.ERL..L..IL..FLE.DS.LD
Retrocopy MVVPSRAMALGELNGSFEWWLDRWLEALGVDTAQHGTNIQGVLQEDIEWERLYVL*VILIPFLEGDSFLD

Parental  ICREIVARWSET-QNVVTKEKK-EDEVQAIATLIEKQAQIVVKPKMVSEEEKQRKAA-LLAQYANVDFQK
          I.REIV..WSE..QNVVTK.K...D..QAI.T...K..QIVVKPK..S.E.KQ.KA..LL.QYANV....
Retrocopy IYREIVEWWSES<QNVVTKQKN>KD*FQAITTVTDKRVQIVVKPKIAS-EKKQWKAI<LLTQYANVTDVE

Parental  SSTDEKDGSVATT--VNIGSEKSLFRNTNVEDVLNARKLERDSLRDESQRKKEQDKLQREKDKLAKQERK
          ...D.KDGSVATT..VN..SEK.L...T.VEDVLNA.KL...SLRDESQRKK.QDKLQREKD.L.KQERK
Retrocopy DEADQKDGSVATTVLVNTVSEKNLSSETHVEDVLNA*KLKGASLRDESQRKKKQDKLQREKDNLSKQERK

Parental  EKEKKRTQKGERK
          EKEKKRTQK.E.K
Retrocopy EKEKKRTQKRECK

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_1378 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1378 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378 ,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173, retro_sscr_944,