RetrogeneDB ID: retro_mdom_1355

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:123196697..123197291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSMODG00000002713
• Aliases: None
• Description: coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]

Sequence

>retro_mdom_1355
CAAGTGACATTCAGGCAGAAGTTTGAAAAGGAAGCAATGGGATCCCTGTCAGATGTTCCAGTTCCCAAATTCAAGCAGGG
AAAAAAGGATATAGCATATGTCCACCGAATGGAACAAGAGGCCCAGCACGTGATCTTCCTCAGTGAGAACCAGGTGGAAC
GGAAACCAGAAAAGGAAGAAACATCTCAGCAAAAGAAATAGAAATCTCAGCGGAAGAAAGGGTTCCAGCATCGACGTTTG
GATAAAGTTAGACAGCAGAAAGAGGAAAAGGCAATAGCCAACCTGGAAAAAGAACTATTTCGAGACTCTGTGAAATTTGG
TGAGGTTGTCCTTCAGCCCCCAGAACTGACAGCAAAACCAAGGAAGAGCATCAGCAGTGACAAGCTTGGCAAGAAATCCC
TGTTGCTGACAAGCCTCCTGGCCCCTGGCAGTGCCCCCCAGCCCTCAGCCGTCTCATTGGCTCGACAACGGATTGTGGCA
GAGGAGAGAGAGCATGTTGTGCAGGCCTACAGGGAGCTAAAGAAATTCAAGCAGCAACAGTTAGAGCAAAGGCAAATCTT
TAACCAAACTGAGAGGAAGCCAAAGAAACCAGCC

Alignment

ORF - retro_mdom_1355 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVTFRQKFEKEAMGSLSDVPVPKFKQGKKESDKAYVHRMEQEAQHVIFLSENQVERKPEKEETSQQKKEK
          QVTFRQKFEKEAMGSLSDVPVPKFKQGKK..D.AYVHRMEQEAQHVIFLSENQVERKP............
Retrocopy QVTFRQKFEKEAMGSLSDVPVPKFKQGKK--DIAYVHRMEQEAQHVIFLSENQVERKPXXXXXXXXXXXX

Parental  SQRKKGFQRRRLDKVRQQKEEKAIANLEKELFRDSVKFGEVVLQPPELTAKPRKSISSDKLGKKSLLLTS
          ...KKGFQ.RRLDKVRQQKEEKAIANLEKELFRDSVKFGEVVLQPPELTAKPRKSISSDKLGKKSLLLTS
Retrocopy XXXKKGFQHRRLDKVRQQKEEKAIANLEKELFRDSVKFGEVVLQPPELTAKPRKSISSDKLGKKSLLLTS

Parental  LLAPGSAPQPSAVSLARQRIVAEERERVVQAYRELKKFKQQQLEQRQIFNQTERKPKKPA
          LLAPGSAPQPSAVSLARQRIVAEERE.VVQAYRELKKFKQQQLEQRQIFNQTERKPKKPA
Retrocopy LLAPGSAPQPSAVSLARQRIVAEEREHVVQAYRELKKFKQQQLEQRQIFNQTERKPKKPA

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_1355 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1355 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355 ,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,