RetrogeneDB ID: retro_mdom_1793

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:130871882..130872368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000023790
• Aliases: None
• Description: None

Sequence

>retro_mdom_1793
TTGACTATGGTGATGTTGAGGCCCCTGACCCTAACTCCTACCAGTAGGAGATGTCAGAGTACCCAATGAAAGTCTTTCAC
CTTTGAAACTGGAAGTCTTCAAAGTGGTCAGTGATGCCTATGAGGAGTCCATGCTTCAGACAGAAAGGAAATGTAGTTCC
AGAATTTTTAACTGCATCTGGGACCTTTGGCAAATACCACTGATAGATTGTCCAATTATCTTAAAGACTGAGCTGAAATT
GATTCTGGAAGTCTTGAAAGAAATTGAAAATCCTGACTTTAAAGATGTTCTGACTCACCTGCTATGAACCCTCAGCCACA
TCTATCAGAAGATCCAAACTGTGTTACTCCTCAACTCTTTAGAAGACACAATCTTCCAGGCTACCAGAACAATTGGCTGT
GCAGTGAGGCCAGGAGAAAATAATCTCAGAGTTGTCTAGAGGCATCTTTCATGCTCACCCTCTTCTGACTCCTTACACAA
GATCTC

Alignment

ORF - retro_mdom_1793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.1 %
• Parental protein coverage: 88.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSMSLTPAPSSLPPEKSCQ-IPQFKSLSPREMEAFTMAKDTYEKSMLQKKRKCSSKFFHRGWDFRQLQLA
          L.M.........P....CQ..P...SLSP...E.F....D.YE.SMLQ..RKCSS..F...WD..Q..L.
Retrocopy LTMVMLRPLTLTPTSRRCQ>VPN-ESLSPLKLEVFKVVSDAYEESMLQTERKCSSRIFNCIWDLWQIPLI

Parental  DRPIVLEAELKLTLEVLKGIQNPELQDVLIQPLQTLSHIYREIQ-SCVTPLPSRGHRLPGRPNNWLHRLT
          D.PI.L..ELKL.LEVLK.I.NP...DVL...L.TLSHIY..IQ..CVTP...R.H.LPG..NNWL....
Retrocopy DCPIILKTELKLILEVLKEIENPDFKDVLTHLL*TLSHIYQKIQ<NCVTPQLFRRHNLPGYQNNWL--CS

Parental  EAGKE-SQSCLEASVMLTLPRLPDTDL
          EA....SQSCLEAS.MLTL..L...DL
Retrocopy EARRK*SQSCLEASFMLTLF*LLTQDL

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_1793 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1793 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008614	1 retrocopy	retro_amel_68,
Canis familiaris	ENSCAFG00000005582	1 retrocopy	retro_cfam_58,
Equus caballus	ENSECAG00000005085	1 retrocopy	retro_ecab_56,
Felis catus	ENSFCAG00000010737	1 retrocopy	retro_fcat_111,
Myotis lucifugus	ENSMLUG00000025607	1 retrocopy	retro_mluc_2004,
Monodelphis domestica	ENSMODG00000023790	1 retrocopy	retro_mdom_1793 ,
Mustela putorius furo	ENSMPUG00000017733	1 retrocopy	retro_mputfur_164,
Tursiops truncatus	ENSTTRG00000003543	1 retrocopy	retro_ttru_769,