RetrogeneDB ID: retro_mdom_442

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:557351708..557352465(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012060
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSMODG00000004326
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_mdom_442
ATGACCCACTTCAACAAGGGCCCTTCTTATGGGCTCTCAGCCGAAGTCAAGAATAAGATTGCCTCCAAATATGACCATCA
GGCAGAGGAAGATCTTCGTAATTGGATAGAAGAAGTTACAGGCTTGAGCATTGGGACAAACTTTCCGCTGGGCTTAAAAG
ATGGCATCATACTCTGTGAACTTATAAACAAGCTACAGCCAGGTTCAGTGAAAAAAGTTAATGAATCTTCATTAAACTGG
CTTCAGTTGGAGAACATTGGTAACTTTATTAAAGCCATTCAAGCTTATGGTATGAAGCCACATGACATCTTTGAAGCAAA
TGATCTCTTTGAAAATGGAAACATGACCCAAGTTCAGACTACATTGGTAGCTTTAGCAGGTCTGGCTAAAACAAAAGGAT
TCCATACGACAATTGACATTGGTGTCAAATATGCAGAAAAGCAAGCGAGGCATTTTTAATGAAGGAAAACTAAAAGCTGG
ACAAAGTGTGATTGGCCTGCAGATGGGAACCAACAAATGTGCCAGCCAGGCAGGAATGACTGCTTATGGGACTAGGAGGC
ATCTTTATGATCCCAAAATGCAAACTGACAAGCCTTTTGACCAGACAACAATTAGTCTGCAGATGGGAACTAACAAAGGA
GCCAGTCAGGCTGGAATGTTAGCACCTGGTACCAGAAGAGACATCTATGATCAGCAGCTAACATTACAACCAGTGAACAA
CTCAAGGATTTCGTTACAGATGGCGACCACTAGATTG

Alignment

ORF - retro_mdom_442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 76.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNFQLGLKDGIILCELINKLQPGSV
          MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNF.LGLKDGIILCELINKLQPGSV
Retrocopy MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNFPLGLKDGIILCELINKLQPGSV

Parental  KKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDI
          KKVNESSLNW.QLENIGNFIKAIQAYG..............NGNMTQVQTTLVALAGLAKTKGFHTTIDI
Retrocopy KKVNESSLNWLQLENIGNFIKAIQAYGXXXXXXXXXXXXXXNGNMTQVQTTLVALAGLAKTKGFHTTIDI

Parental  GVKYAEKQARR-FDEGKLKAGQSVIGLQAIMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ
          GVKYAEKQAR..F.EGKLKAGQSVIGLQ..MGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ
Retrocopy GVKYAEKQARH>FNEGKLKAGQSVIGLQ--MGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ

Parental  MGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKV
          MGTNKGASQAGMLAPGTRRDIYDQ.LTLQPV.NS.ISLQM.T...
Retrocopy MGTNKGASQAGMLAPGTRRDIYDQQLTLQPVNNSRISLQMATTRL

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	7.51 RPM	0.00 RPM
SRP007412_cerebellum	9.47 RPM	0.00 RPM
SRP007412_heart	2.19 RPM	0.00 RPM
SRP007412_kidney	35.55 RPM	0.00 RPM
SRP007412_liver	16.62 RPM	0.00 RPM
SRP007412_testis	3.14 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_442 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_442 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 19 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus	ENSDNOG00000012883	3 retrocopies	retro_dnov_223, retro_dnov_403, retro_dnov_815,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442 ,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,