RetrogeneDB ID: retro_mdom_1473

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:209487505..209487952(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS2
• Ensembl ID: ENSMODG00000017882
• Aliases: None
• Description: HAUS augmin-like complex, subunit 2 [Source:HGNC Symbol;Acc:25530]

Sequence

>retro_mdom_1473
TTGGAAATTTACCTCTTAATACTTGAAAAGCATACAACAGATGCCATTCATCCTTTCTTTCTAATTCAAAAGTGCAAGAC
TCTGCAAAGTACAAATCAACACTTGGAGACGGTGCTGAAGGAGAAAACAGTCTTCTGAAAGAGACTAATGAAACCTCCTG
TGTCAGGAAAACTTGCCTATTGAAGCTGAATACTACAGGTATGTGCGACAATTGCTGAAGTTATCACTGACTTTCATTGA
GACACTAGAAGCTCATGTTGATGACATTAGAAGCATTCCTTATTTAGAATCCAGTGTGAAAAATATGTTTTAGGATAGGA
CTTTGACAAAAATGAATGTATTGGTGGGAGAGATAGAAGAACTAGGAGAAAACATGCTCAAGTGGTGAAAACAACAAAAG
GAAATTTCTCCTATCACCAATATTTCCTTGAGTTTATCTTCAAAAAA

Alignment

ORF - retro_mdom_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.13 %
• Parental protein coverage: 68.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LELDLLTLEKDTADVVHPFFLAQKCEALQNMNQHLETVLKEKKALRHRLMKP-LCQENLAIEAIYHRYVV
          LE..LL.LEK.T.D..HPFFL.QKC..LQ..NQHLETVLKEK.....RLMKP.LCQENL.IEA.Y.RYV.
Retrocopy LEIYLLILEKHTTDAIHPFFLIQKCKTLQSTNQHLETVLKEKTVF*KRLMKP>LCQENLPIEAEYYRYVR

Parental  QLLDLAVNFIEKLESHVETIRNIPCLDSSVKNM--DRALTRMTVLEGETEQLIENILKWREQQKEISSSI
          QLL.L...FIE.LE.HV..IR.IP.L.SSVKNM..DR.LT.M.VL.GE.E.L.EN.LKW..QQKEI.S.I
Retrocopy QLLKLSLTFIETLEAHVDDIRSIPYLESSVKNMF*DRTLTKMNVLVGEIEELGENMLKW*KQQKEI-SPI

Parental  TKL-FSEDLFKK
          T...F.E..FKK
Retrocopy TNI<FLEFIFKK

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	28.37 RPM
SRP007412_cerebellum	0.00 RPM	29.71 RPM
SRP007412_heart	0.00 RPM	80.94 RPM
SRP007412_kidney	0.00 RPM	117.20 RPM
SRP007412_liver	0.00 RPM	62.94 RPM
SRP007412_testis	0.00 RPM	100.77 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1473 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1473 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003587	4 retrocopies	retro_meug_1171, retro_meug_1231, retro_meug_702, retro_meug_996,
Microcebus murinus	ENSMICG00000000819	1 retrocopy	retro_mmur_648,
Monodelphis domestica	ENSMODG00000017882	1 retrocopy	retro_mdom_1473 ,
Oryctolagus cuniculus	ENSOCUG00000011004	1 retrocopy	retro_ocun_1322,
Sorex araneus	ENSSARG00000001275	2 retrocopies	retro_sara_123, retro_sara_413,
Ictidomys tridecemlineatus	ENSSTOG00000006207	1 retrocopy	retro_itri_618,
Vicugna pacos	ENSVPAG00000006260	1 retrocopy	retro_vpac_599,