RetrogeneDB ID: retro_mdom_702

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:160960808..160961338(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017091
• Aliases: None
• Description: None

Sequence

>retro_mdom_702
TGTCACCCATGAAGAGTTCTTCACAGAGATTTGAATCCTCAAAATCTACTAATAGATGATAAAGGTATAATTAAACTAGC
TGATTTTGTTCTTGTATTGGAATATCTTTGAGGGTATACACATATCAGGTGGAAATAGTATAGTATCAGTCTCCAAAAGT
ATTGCTAGAAAAGGCCAGACATTCTATTCCAGTAGACATTTGGTACATAGGCACAGTGTTTGCTGAATTAGCAACCAAGA
AGCCACTTTTCGACAGAGATTCTGAAACTGACTAGCTTTTCCAAATCTTCAGGGCTTTGGGGACTCTTAATAATAAAGTG
TGGCCAGAAGCTGAGTCATTTCAGGATTCCAAGAATATATTCCCCAAGTGGAAATCAGGAAGTCTGATGTCACATGTCAA
GAACCCCAAGAAAACAACATCAATTTCCTCTCTAAAAAGGTTAGTCTATGATTCTGCCAAGCAAATTTCTGGCAAAATGG
CATGGAACCATCCACGTTTTAATGACCTGGACAGTCAGATTAAGAAGCTC

Alignment

ORF - retro_mdom_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 59.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CHSRRVLHRDLKPQNLLIDDKGVIKLADFGLARAF-GIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDI
          CH..RVLHRDL.PQNLLIDDKG.IKLADF.L...........Y..E.V...Y.SP.VLL..AR.S.PVDI
Retrocopy CHP*RVLHRDLNPQNLLIDDKGIIKLADFVLVLEY<SLRVYTYQVEIV--*YQSPKVLLEKARHSIPVDI

Parental  WSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLTSHVKN-L
          W.IGT.FAELATKKPLF..DSE.D.LF.IFRALGT.NN.VWPE.ES.QD.KN.FPKWK.GSL.SHVKN..
Retrocopy WYIGTVFAELATKKPLFDRDSETD*LFQIFRALGTLNNKVWPEAESFQDSKNIFPKWKSGSLMSHVKN<P

Parental  DENGIDLLS-KMLVYDPAKRISGKMALNHPYFNDLDSQIKKL
          .EN.I..LS.K.LVYD.AK.ISGKMA.NHP.FNDLDSQIKKL
Retrocopy QENNINFLS>KRLVYDSAKQISGKMAWNHPRFNDLDSQIKKL

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	0.95 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.40 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	1.51 RPM
SRP007412_testis	0.00 RPM	20.43 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_702 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_702 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000007835	1 retrocopy	retro_mdom_32,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702 ,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,