RetrogeneDB ID: retro_mdom_891

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:339273512..339274440(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSMODG00000002466
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_mdom_891
CAGATGGATTTACAGCAGGAATTCTATGAAACAACACTGAGAGCTCTGAGAAATGCTAAGAATGATAGGCTGTGGTTTAG
GACAAACACAAAGCATGGAAAATTCTATCTAGAATGAGAAGAATATAGAAAGCGTCAAAAAATTTTGCACCAGTTGCATC
AGTCATATCAAATAGATGATGAAGATGACCTTAAAAAGATATACAATTATTGGAAATTTAAGCATTAGAAATTCAAATGT
ATACAGCACAGAAAAATTACAAAAAATTCAAAACATCATATAGACAATCACTGCATAACAAGTCAGTCATCTCCCATCCA
CTGATCATGGGTGTCATTAGAAAATGTGTTGGTAAAATGCACTTAAGAGAAGGTGAATTTGAGAAGGCTCACAGTGATTG
TTTTTGAAGCATTCAAGAATGAGAATGAAGTCAGGTAAGTCCAGATGAAGCACTAGCTTAAAATATTTGATCTTAGCAAA
CATGCTAAACATACTAATGAAGCTGGGAATAAATCCATTTGATTCTCAGGAAGTAAAGCCATAGAAAAATGATCCAGAGA
TTCTAGCAATGATGAATTTAGTTAAGTGCCTGTCAGAATAATAGCATCACCTACTTTGAGAAGATTCTGAAAACAAATCA
CAGCAATGTCAGGGGCAATCCTGTCATAAGAGAGCACATCAAAAAGCTTTTGCAAAACATCAGAAAACAAGTACTTATAA
AATTGTCTTACACAAGAATACATATTTCTTTTATTTTAGAGAATTAAACATAGATGTAGCTGAAATAAAGAATTTACTAA
TCCAATGTATATTGGATAATATTCATGGTTGAATTGATCAAGTCAAAAAGCTCCTAGAATGGGATCATCAAAAGGGGAAC
AATGTCCAGTATGCTGCACTAGATAAACAGACCAACCAGCTAAATTCT

Alignment

ORF - retro_mdom_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.58 %
• Parental protein coverage: 68.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKK-GT
          QMDL.QEFYETTL.AL..AKNDRLWF.TNTK.GK.YLE.EEY.K.QKIL.QLHQS.Q.DD.EDDLKK...
Retrocopy QMDLQQEFYETTLRALRNAKNDRLWFRTNTKHGKFYLE*EEYRKRQKILHQLHQSYQIDD-EDDLKK<DI

Parental  QLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTD-FFEA
          QLLEI.ALEIQMYTAQKN.KK.K..Y.QSLH.KS.I.HPLIMGVIR.C.GKMHLREGEFEKAH.D..FEA
Retrocopy QLLEI*ALEIQMYTAQKNYKKFKTSYRQSLHNKSVISHPLIMGVIRKCVGKMHLREGEFEKAHSD>VFEA

Parental  FKNYDE-SGSPRRTTCLKYLVLANML---MKSGINPFDSQEAKPYKNDPEILAMTNLV-SAYQNNDITEF
          FKN..E.SG..R..T.LKYL.LANML...MK.GINPFDSQE.KP.KNDPEILAM.NLV.SA.QNN.IT.F
Retrocopy FKNENE>SGKSR*STSLKYLILANMLNILMKLGINPFDSQEVKP*KNDPEILAMMNLV>SACQNNSITYF

Parental  EKILKTNHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFI-SKELNIDVADVESLLVQCILD
          EKILKTNHSN....P.IREHI..LL.NIR.QVLIKL...YTRIHI.FI...ELNIDVA....LL.QCILD
Retrocopy EKILKTNHSNVRGNPVIREHIKKLLQNIRKQVLIKL--SYTRIHISFI<FRELNIDVAEIKNLLIQCILD

Parental  NTIHGRIDQVNQLLELDHQKRGGARYTALDKWTNQLNS
          N.IHG.IDQV..LLE.DHQK.....Y.ALDK.TNQLNS
Retrocopy N-IHG*IDQVKKLLEWDHQKGNNVQYAALDKQTNQLNS

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	238.27 RPM
SRP007412_cerebellum	0.00 RPM	215.79 RPM
SRP007412_heart	0.00 RPM	270.72 RPM
SRP007412_kidney	0.00 RPM	422.70 RPM
SRP007412_liver	0.00 RPM	242.18 RPM
SRP007412_testis	0.00 RPM	421.74 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_891 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_891 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891 ,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,