RetrogeneDB ID: retro_mdom_506

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:81322891..81323405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD5
• Ensembl ID: ENSMODG00000016596
• Aliases: None
• Description: potassium channel tetramerization domain containing 5 [Source:HGNC Symbol;Acc:21423]

Sequence

>retro_mdom_506
TCTGGGCTCAAGCTCCTCGGGAGCACGCAGCAGGCAGTGATTCCAAATCGGCCTGACTCTACGTGGGCGGCAACTACCTC
ATCACTACCCAGCAGCATCTCTGCCGGAACCAGAAGTCCTTCCTGTAGCGCCTGCGCCAGGCAGATCTGGACTTGAACTC
GGACAAAGAAGAAACTGGTCCCTGTTTAATAGACAAGAGATTCCCCCCTATTTGGAGCCAGTCCTGAACTACTTGAGGCA
TGGAAAACTGGTCATTAATAAGGACCTTGCAAAGGGGATGCTGGAGGAAGCTGAATTTTATAACATCACTTTAGTAATAA
AACTTGCAAAGGACAAAATTAGAGAACGGAACAGCAAAACATTACAGGTGCCAGTCAAGCATGTCTATAGAGTGCTCCAT
TGTCCAGACAAAGAGCTTCCCCAAATGGTTTCAACCATGTCTGATGGCTAGAAGTTTGAGCAATTGGTCAGTATTGGTTC
ATTTTATAACTTTGGATATGAAGACTAAGCTGAG

Alignment

ORF - retro_mdom_506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 71.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGLAPLG-ERATGGGSKWVRLNVGGTYFLTTRQTLCRDPKSFLYRLCQADPDLDSDKDETGAYLID-RD-
          SGL..LG.E.A.G..SK...L.VGG.Y..TT.Q.LCR..KSFL.RL.QAD.DL.SDK.ETG..LID.RD.
Retrocopy SGLKLLG<EHAAGSDSKSA*LYVGGNYLITTQQHLCRNQKSFL*RLRQADLDLNSDKEETGPCLID>RD>

Parental  PTYFGPVLNYLRHGKLVINKDLAEEGVLEEAEFYNITSLIKLVKDKIRERDSKTSQVPVKHVYRVLQCQE
          P.Y..PVLNYLRHGKLVINKDLA..G.LEEAEFYNIT..IKL.KDKIRER.SKT.QVPVKHVYRVL.C..
Retrocopy PPYLEPVLNYLRHGKLVINKDLAK-GMLEEAEFYNITLVIKLAKDKIRERNSKTLQVPVKHVYRVLHCPD

Parental  EELTQMVSTMSDGWKFEQLVSIGSSYNYGNEDQAE
          .EL.QMVSTMSDG.KFEQLVSIGS.YN.G.ED.AE
Retrocopy KELPQMVSTMSDG*KFEQLVSIGSFYNFGYED*AE

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_506 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_506 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019357	1 retrocopy	retro_cfam_433,
Homo sapiens	ENSG00000167977	1 retrocopy	retro_hsap_2224,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Monodelphis domestica	ENSMODG00000016596	1 retrocopy	retro_mdom_506 ,
Sarcophilus harrisii	ENSSHAG00000006867	1 retrocopy	retro_shar_158,
Ictidomys tridecemlineatus	ENSSTOG00000006647	8 retrocopies	retro_itri_1562, retro_itri_1690, retro_itri_1692, retro_itri_1761, retro_itri_1779, retro_itri_1844, retro_itri_1889, retro_itri_950,
Tursiops truncatus	ENSTTRG00000008237	1 retrocopy	retro_ttru_1510,