RetrogeneDB ID: retro_mdom_1841

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:60651937..60653547(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000020503
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSMODG00000005252
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_mdom_1841
ATGGCGCTGACCAGCTTTTTACCTGCTCCAACGCAGCTTTCTCAGGACCAGCTTGAAGCTGAGGAAAGAGCACGATCACA
GAGATCAAGGCAGACTGCTCTGGTCTCATCACGAAGAGAACCTCCACCTTATGGGTATCGAAAAGGTTGGATACCTCGTT
TGTTAGAGGATTTTGGAGATGGCGGTGCCTTTCCAGAAATACACGTGGCCCAATACCCATTGGATATGGGAAGAAAGAAG
AAAATGTCCAATGCATTGGCCTTTCAAGTGGATGCAGAGGGAAAAATTAAATATGATGCAATTGCTCGACAGGGACAATC
AAAGGACAAGGTCATTTATAGCAAGTATACTGACCTGGTTCCCAAAGAAGTTATGAATGCAGATGACTCAGACCTACAAA
GACCTGATGAAGAAGCCATTAAAGAGATTACAGAAAAGACACGAGTAGCCCTAGAGAAATCTGTGTCTCAGAAGGTTGCT
GCTGCTATGCCAGTTCGAGCTGCAGATAAACTAGCTCCAGCTCAGTATATCCGGTATACACCATCTCAGCAAGGAGTGGC
TTTCAATTCTGGAGCTAAGCAAAGAGTTATTCGAATGGTGGAAATGCAAAAAAGATCCAATGGAGCCTCCAAGATTCAAG
ATTAATAAGAAAATTCCTCGTGGATCTCCTTCTCCTCCTGCACCTGTCATGCATTCTCCTAGCCGAAAGATGACTGTGAA
GGAGCAGCAAGAGTGGAAAATTCCTCCTTGTATTTCAAACTGGGAAAAATGCAAAGGGCTATACTATTCCATTAGACAAA
CGTCTGGCTGCTGATGGGAGAGGACTGCAAACAGTTCACATTAATGAAAACTTTGCCAAACTTGCTGAAGCTCTCTACAT
TGCTGATAGAAAGGCTCGTGAGGCAGTAGAGATGCGTGCTCAAGTGGAAAGAAAGATGGCCCAAAAAGAAAAGGAGAAAC
ATGAAGAGAAGCTTCGAGAAATGACCCAGAAAGCTCGGGAGAGGAGAACTGGAATCAAGACCCACGTAGAAAAAGAGGAT
GGAGAGGCTCGTGAACGGGATGAAATAAGACATGATAGATGCAAAGAAAGACAGCATGACAGGAATCTTTCCAGAGCAGC
TCCTGATAAGAGGTCAAAACTCCAGAGAAATGAGACTCGAGATATCAGTGAAGTCATTGCTCTTGGTGTGCCCAATCCTC
GGACTTCCAATGAAGTTCAGTATGACCAGAGATTATTCAACCAGACTAAGGGCATGGACAGTGGTTTTGCTGGCTGAGAG
AATGAAATTTATAATGTTTATGATCAACCATGGAGATGTGGCAAAGACATGGCCCAAAATATCTACAGACCCAGTAAAAA
TTTGGACAAAGACATGTATGGTGATGACCTAGAGGCCCGAATAAAGACCAATAGATTTGTTCCTGATAAGGAGTTCTCTG
GCTCAGATCATAGGCAGAGAGGCTGAGAAGGACCAGTTCAATTTGAGGAAGATCCCTTTGGTCTGGACAAATTTTTGGAA
GAAGCCAAACAGCATGGAGGGTCTAAAAGACCCTCAGATAGCAGTCGCCCGAAGGAACACGAACATGAAGGCAAGAAGAG
GAGGAAGGAG

Alignment

ORF - retro_mdom_1841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALTSFLPAPTQLSQDQLEAEERARSQRSRQTALVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
          MALTSFLPAPTQLSQDQLEAEERARSQRSRQTALVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
Retrocopy MALTSFLPAPTQLSQDQLEAEERARSQRSRQTALVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA

Parental  QYPLDMGRKKKMSNALAIQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAI
          QYPLDMGRKKKMSNALA.QVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADD.DLQRPDEEAI
Retrocopy QYPLDMGRKKKMSNALAFQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDSDLQRPDEEAI

Parental  KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQK-DPMEP
          KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQK.DPMEP
Retrocopy KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQK>DPMEP

Parental  PRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNW-KNAKGYTIPLDKRLAADGRGLQTV
          PRFKINKKIPRG.PSPPAPVMHSPSRKMTVKEQQEWKIPPCISNW.KNAKGYTIPLDKRLAADGRGLQTV
Retrocopy PRFKINKKIPRGSPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNW>KNAKGYTIPLDKRLAADGRGLQTV

Parental  HINENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGE
          HINENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREM.QKARERR.GIKTHVEKEDGE
Retrocopy HINENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMTQKARERRTGIKTHVEKEDGE

Parental  ARERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNETRDISEVIALGVPNPRTSNEVQYDQRLFNQTKGM
          ARERDEIRHDR.KERQHDRNLSRAAPDKRSKLQRNETRDISEVIALGVPNPRTSNEVQYDQRLFNQTKGM
Retrocopy ARERDEIRHDRCKERQHDRNLSRAAPDKRSKLQRNETRDISEVIALGVPNPRTSNEVQYDQRLFNQTKGM

Parental  DSGFAGGEDEIYNVYDQPWRSGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGR
          DSGFAG.E.EIYNVYDQPWR.GKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSD.RQRG.
Retrocopy DSGFAG*ENEIYNVYDQPWRCGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDHRQRG*

Parental  EGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
          EGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
Retrocopy EGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE

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	163.30 RPM
SRP007412_cerebellum	0.00 RPM	158.00 RPM
SRP007412_heart	0.00 RPM	102.87 RPM
SRP007412_kidney	0.00 RPM	130.37 RPM
SRP007412_liver	0.00 RPM	152.56 RPM
SRP007412_testis	0.00 RPM	225.51 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1841 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1841 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 21 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841 ,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,