RetrogeneDB ID: retro_mdom_597

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:449125098..449125862(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSMODG00000017860
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_mdom_597
GGGGATGTTGAAAATTACTACTATGGTCAGGGTCACCCAATGAAACCCCATCGAATCTGAATGACTCACAACTTGCTACT
AAACTATGGACTCTACCGAAAGATGGAAATATATAGGCCCCACAAAGCCCATGCTGATGAGATGACCAAGTACCATGATG
ATGACTACATTAAGTTTTTGTGCTCGATCCATCCTGATAATATGTTGGAGTACAGCAAACAATTGCAGAGATTTAATGTT
GGTGAAGACTGCCCGGTGTTTGATGGCTTGTTTGAGTTCTGTCAATTATCCACCAACGGATCTGTGGCAAGTGCAGTGAA
GCTTAGTAAACAGCAGATGGATATTGCTGTGAACTGGGCTGGGGGCCTGCACCATGCTAAGAAGTCTGAAGCATCTGGCT
TCTGCTACATCAATGATATTGTGTTGGCCATCCTGGAACTGTTAAAGTACCACCAGAGGGTGCTGATATTGACATTGGCA
TTCACCATGGCGATGGCGTGGAAGAAGCTTTCTACACCACAGATCGGGTCATGACAGTGTCCTTTCATAAGTATGGAGAG
TACTTCCCGGGAATGGGGGACCTATGGGACATTGGAGCTGGCAAAAGCAAATACTATACTGTTAACTACCCGCTTCAAGA
TGGGATTGATGATGAATCTTATGAGGCCATCTTCAAACCAGTTATGTCCAAGGTAATGGAGAATTTTCAGCCTAGTGCAG
TGGTCTTGCAGTGTGATTCTGATTCTCTGTCTGGAGACCGCTTG

Alignment

ORF - retro_mdom_597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 52.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSE
          GD..NYYYGQGHPMKPHRI.MTHNLLLNYGLYRKMEIYRPHKA.A.EMTKYH.D.YIKFL.SI.PDNM.E
Retrocopy GDVENYYYGQGHPMKPHRI*MTHNLLLNYGLYRKMEIYRPHKAHADEMTKYHDDDYIKFLCSIHPDNMLE

Parental  YSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDI
          YSKQ.QRFNVGEDCPVFDGLFEFCQLST.GSVA.AVKL..QQ.D.AVNWAGGLHHAKKSEASGFCY.NDI
Retrocopy YSKQLQRFNVGEDCPVFDGLFEFCQLSTNGSVASAVKLSKQQMDIAVNWAGGLHHAKKSEASGFCYINDI

Parental  VLAILELLKYHQRVLY-IDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVN
          VLAILELLKYHQRVL..IDI.IHHGDGVEEAFYTTDRVMTVSFHKYGEYFPG.GDL.DIGAGK.KYY.VN
Retrocopy VLAILELLKYHQRVLI<IDIGIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGMGDLWDIGAGKSKYYTVN

Parental  FPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRL
          .P..DGIDDESY..IFKP..SKVME..QPSAVVLQC..DSLSGDRL
Retrocopy YPLQDGIDDESYEAIFKPVMSKVMENFQPSAVVLQCDSDSLSGDRL

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	1.07 RPM	0.00 RPM
SRP007412_cerebellum	2.29 RPM	0.00 RPM
SRP007412_heart	2.59 RPM	0.00 RPM
SRP007412_kidney	3.95 RPM	0.00 RPM
SRP007412_liver	4.53 RPM	0.00 RPM
SRP007412_testis	14.34 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_597 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_597 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597 ,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,