RetrogeneDB ID: retro_mdom_1032

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:298360055..298361041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSMODG00000020386
• Aliases: None
• Description: BRX1, biogenesis of ribosomes, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24170]

Sequence

>retro_mdom_1032
ATGGTGGCGATCAAGAGGAAGCAATACGAAATAGGAGGTCCTGAGGTGAAGAAGCCAAAAGAGAAGGGGGAAAAGGCAAG
AGCTCATGCCAAACCACTCCCTCTGGCCCCAGGGAAGGCAGAGGGAGAGGAGTACCATATCCCCTGCCCAGTCTAAGGGT
AAATGGAAGAATTAGGAATGAATTCTTATCTTCTCATCAAGGAGAATAAATTTCATAACAGGACACAATTCAAGATTTAA
GAACACTGATGCCTCATTCTAAAGCAGATAACAAAATGGACCAGAAGGATAAATTGTTTGTATTTTATGAGGTCTGTGAA
ATAAAAAAAAAGAACTTTAATAAAGGTATCTATTTTGAAGATAAGAAAAAACAGGATCTCTATATGTGGCTTTCAAATTC
ATCTCAAGGACCTTTGGCTAAGTTCTTAGTTCAGAATATACATACTTTGACAGAGTTAAAGATGACTGGAAACTGTTTTA
AGAAGTTCACAACCTCTTCTGTCTTTTGATCCTTCTTTTGATGAATCACCACATTATTATTTGATAAAATTACTCCTTAT
TCAGATATTTTGTACTCTTCAATACCATCCCAAAAGCCAACCATTTGTTAACCTTGTGTTTATCTTTATCAGTATGGATC
ATAGGATCTGTTTTTTTTTACTACCAGATCATAGAGGAAGATGCAGCTCTTGTAGAAATTGCACCTCATTTTGTCTTGAA
TCTCATAAAGATTTTCCAAGGCAGCTTTGGAGGACCAACTTTCATGAAAATCCACATGATCAGTCACTAAACATGCATCA
GGGTATAATGAGAATGGCCACAGCTACAAAATACAGGGAGAGACAACAAGTCAAAGATGTACAGACACTCAACAAAAAAA
AGATAAAACTATTATTCCAGAAGATTATGCTGATGATGTTTTTAAGTCACCAGTTTAAGAAAAGTGAGTGGAAATACTCT
TTGTGGAAGCAGAGCCCAAAGTCAGT

Alignment

ORF - retro_mdom_1032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.55 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVAIKRKRHGGGGPEAKKPKGKGKETRAPAKPLPVA-PGKAEGEE-EYRIPGPVTKGKWKNKERVLIFSS
          MVAIKRK....GGPE.KKPK.KG...RA.AKPLP.A.P....G....Y..P.....G...N.......S.
Retrocopy MVAIKRKQYEIGGPEVKKPKEKGEKARAHAKPLPLA<PREGRGRGVPYPLPSLRVNGRIRNE---FLSSH

Parental  RGINFRTRHLMQDLRTLMPHSKADNKMDRKDKLFVINEVCEIK--NCNKCIYFEAKKKQDLYMWLSNSPQ
          .G.........QDLRTLMPHSKADNKMD.KDKLFV..EVCE....N.NK.IYFE.KKKQDLYMWLSNS.Q
Retrocopy QGE*IS*QDTIQDLRTLMPHSKADNKMDQKDKLFVFYEVCEXXXXNFNKGIYFEDKKKQDLYMWLSNSSQ

Parental  GPSAKFLVQNIHTLAELKMTGNC-LRGSRPLLSFDPTFDESPHYSLIKELFIQIFCTPQYHPKSQPFVDH
          GP.AKFLVQNIHTL.ELKMTGNC.LR.S.PLLSFDP.FDESPHY.LIK.L.IQIFCT.QYHPKSQPFV..
Retrocopy GPLAKFLVQNIHTLTELKMTGNC>LRSSQPLLSFDPSFDESPHYYLIKLLLIQIFCTLQYHPKSQPFVNL

Parental  VFTFTIMDNRI-WFRNYQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPT-LYENPHYQSPNMHRRIVRMT
          VF.F..MD.RI.....YQIIEEDAALVEI.P.FVLNLIKIFQGSFGGPT...ENPH.QS.NMH..I.RM.
Retrocopy VFIFISMDHRI>XXXXYQIIEEDAALVEIAPHFVLNLIKIFQGSFGGPT<FHENPHDQSLNMHQGIMRMA

Parental  TAAKYRERQQVKDVQRL-KKKEDKTIIPEDPTDDVFKTPAEEKPVEILFVKPEPKVS
          TA.KYRERQQVKDVQ.L.....DKTIIPED..DDVFK.P..EK.VEILFV..EPKVS
Retrocopy TATKYRERQQVKDVQTL<QXXXDKTIIPEDYADDVFKSPV*EK*VEILFVEAEPKVS

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	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1032 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1032 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032 ,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,